Finally finished, and in random order, is the Naruto vs. Real Life wiki. I hope this helps anyone who is interested. I tried to keep it concise and to the point.

Contents (Use ctrl-F to find topics using the numbers):
1.1 Tree walking
1.2 Water Walking
1.3 Chakra
1.4 Major summons and the Sannin
1.5 Eye techniques
1.6 Gentle Fist
1.7 Swords
1.8 Kunai
1.9 Shuriken
2.0 Girls
2.1 Shadow Clones
2.2 Villages and ranks
2.3 Temari’s Kamaitachi
2.4 Sandaime’s Nyoubou
2.5 Tailed beasts
2.6 Symbols
2.7 Hand seals
2.8 Puppets
2.9 Explosives

1.1 Tree Walking
Historical ninja attached ashiko spikes to the bottom of their jika-tabi (Ninja shoes, look like normal tabi socks with a separate big toe, wound with thick string to make sandals that could be removed with a single tug at a secure loose end.) With these they could climb walls or trees easily to infiltrate an enemy castle, or scout from atop a tree.

1.2 Water Walking
Not content with just tree climbing, ninja’s also found a way to walk on water. Behold, the water walking shoe: http://japundit.com/wp-content/uploads/2006/05/water%20walking%20shoe1.JPG
These shoes came in many styles, the one in the picture being called “kumo/spider” style. This, along with a pole of your choice, became an excellent way to cross castle moats and swamps. The amount of balance needed to use them is astounding, especially if you chose not to have a pole.

1.3 Chakra
In Japanese martial arts it is believed that if you train hard enough you can master and control an inner power known as ki or chi. Hence fighting styles such as Aikido, which train practitioners from the word go about how to control ki, which allows them to gain large amounts of strength without using force. I used to do aikido, and I remember my sensei telling me to push over a line of people, all trying their hardest not to get pushed over. Of course I couldn’t do it using my muscles, so she told me to close my eyes and focus on imagining that my hand was travelling through the wall, through the air until I reached a tree miles away, and when I had, she asked me to push again, and without any effort at all they were all on the floor. We all took it in turns to push and be pushed using ki and everyone succeeded, and we were only white belts. This is the origin of the concept of chakra in Naruto. However, chakra is another type of inner force used in Buddhist meditation. There are many different beliefs about chakra, but the most common and modern one is that there exists seven types of chakra in different locations in the body:
Red - Behind the genitals - Symbolises physical needs, for food, wealth, ect.
Orange - The base of the spine - Feelings and sexuality.
Yellow - The solar plexus/navel - Individuality
Green - The heart - Love and compassion
Blue - The neck - Communication and expression
Violet - The forehead - The third eye, insight and visualization
Pure white/colourless - Above the centre of the head - Wisdom, perfection, Nirvana.
Illnesses in new-age thinking are sometimes thought to be the cause of imbalanced chakra, and can be cured through meditation and re-balancing methods. I don’t know much else about it, I’m afraid.

1.4 Major summons and the Sannin
The three Sannin, Tsunade, Jiraiya and Orochimaru all appear in an old Japanese tale entitled The Legend of Gallant Jiraiya. In it, Jiraiya is the heir to a powerful ninja clam, who can morph himself into a giant toad. He falls in love with a princess named Tsunade, who was a master of snail magic, and marries her. One of Jiraiya’s followers, Yashagoro, was enticed by snake magic and changed his name to Orochimaru, and battled Jiraiya and Tsunade for power. Orochimaru was killed, but the two fell unconscious from the venom. Moments from death, a follower of Jiraiya who he had once saved came to their aid, and rescues them. The tale ends here, prematurely. In Japanese culture, the Snail/slug, toad and snake are in essence incompatible, and unable to defeat each other, their relationship is sort of like Jakenpo (Rock, paper, scissors).

1.5 Eye techniques
Eye techniques - Dojutsu - such as Sharingan and Byakugan are seen often in modern Japanese anime/manga/fantasy novels, however I have never found any evidence linking it to history or culture. One notable thing though is that pure white byakugan-like eyes are seen on Daruma dolls - You use black ink to paint one pupil to symbolise starting a task or a wish, and colour in the other pupil when it is completed. This may be a long shot but Neji often wishes to be free, as does Hinata, of their positions in life. Though, Daruma are often considered to be optimistic, so I guess the similarity ends there.

1.6 Gentle Fist
Although real ninjutsu would be, in the Naruto world, simply taijutsu, a number of moves are seen in both. For instance, the Hyuuga clan’s gentle fist, used to hit chakra points to immobilise an opponent, is similar to a Shobo ring, which has a slight wooden point, worn by the ninja to hit the enemies pressure points and cause temporary paralysis.

1.7 Swords
Ninja swords, shinobigatana, were shorter than the average samurai sword (Unlike the massive shinobigatana of the Hidden Mist), but were used more as tools than weapons. There’s a technique, which is hard to describe in writing, for scouting a pitch black area for enemies. The sword’s scabbard is balanced on the tip of the outstretched sword, held on by string attached to it, held in the ninja’s teeth, so that the length of the outstretched sword is doubled. If the ninja feels it touch an enemy, before they can react, he lets go of the string and lunges forward with the sword. Other than for this or similar sneaky techniques, there was also the Shikoro ken, saw sword, used to saw through walls.

1.8 Kunai
Kunai may be the most used weapon on Naruto, but they were far from it in real life. Their name means “gouger”, and they were used for exactly that. Gouging holes out of castle mortar, to make footholds for climbing, or gouging holes straight through flimsy walls. Every self-respecting ninja had one in his pack, but they were never intended as a weapon.

1.9 Shuriken
Used pretty much as they are in Naruto, same with needles. It would be impossible, and downright fatal, to keep poisoned needles in your mouth like Shizune however.

2.0 Girls
In Ancient Japan traditionally girls were not trained to be full ninjas in a ninja village, though often the more capable (ie - not married) ones were trained to spy, poison, and seduce. Like it or not, female ninja were often disguised as prostitutes or courtesans to allow them into the inner reaches of a lord’s castle, giving them an excellent opportunity to map out the interior and overhear conversations. If the worst happened, they were trained in close-range fighting using thin blades tucked up their sleeves or hidden in their fans. They were called Kunoichi - If you take the Japanese character for female, and remove the individual strokes into a separate word, it spells kunoichi. However, it probably came from Kunoichi meaning “Dragon Lady” instead. In the 1850’s Ninja were seen as too dangerous to keep, so attempts were made to destroy them, by demolishing their villages, killing their families and making organized ninjutsu illegal. However, the daughter of an assassinated ninja head, after pleading ignorance and marrying into her family’s killers, invited them all around to dinner and subsequently poisoned them all. She then became the clan leader, and became known as the dragon lady, Kunoichi.

2.1 Shadow Clones
In Japanese Kabuki theatre, ninja’s were often dressed in black, and often many people were on the stage at one time representing the same ninja. Black clothing in Kabuki means that the person is invisible, so the audience ignores them, until they turn round and play the ninja. Often the moves they had to make were too hard for one actor to do alone so other actors would help them by lifting them in the air or taking their place as the character somewhere else on the stage. This can be seen really well (and funnily) here: http://uk.youtube.com/watch?v=Nh0SYUknsI0

2.2 Villages and ranks
Ninja villages did exist, and they were hidden too. Ninja were the product of two areas of Japan: Ida and Kouga, and you can go there to see recreations of Ninja houses and villages. Disguised as small farming villages, they looked completely normal. However, if you looked from above you see that the flooded rice fields don’t lie in one area, but all around the village as a sort of moat that could contain traps and hidden weapons for ease of use. They still used them for food, but the farmers were more than likely guard ninja or ninja not currently on missions, as the whole village’s children were trained in ninja arts. Houses often contained hidden rooms or trapdoors leading to where that family kept their equipment or secret ninja scrolls (Containing written descriptions of secret techniques to be passed down - Like Itachi telling Sasuke where the Uchiha family’s secret was.) There were Genin and Chuunin, too. Genin were the ones sent out on missions while the Chuunin were more like ANBU, or sorted out affairs at home. The leader was called the Shonin, his house was often the biggest, most heavily guarded. He wasn’t necessarily the strongest, he just had to be the head of the main family. It wasn’t uncommon for children as young as 12 to be sent on missions, their training started the moment they were able to walk. Training for young ninja’s included being left in the wilderness with a bag of rice and a knife, to fend for themselves and find their way back, shuriken training as seen in Naruto academy flashbacks, testing how long they could breathe underwater, tree climbing using foot spikes and combat training using logs.

2.3 Temari’s Kamaitachi
For those that don’t remember, Kamaitachi is the name of Temari’s sickling winds attack. It means literally “Sickle weasel”. Originally Kamaitachi was a name for a particularly strong gust of wind, which would seem to cut the person feeling it, but they would never see any wound. This is because kamaitachi worked in threes, with the first weasel knocking the person down with the gust, the second cutting the person on their bare skin, and the third applying medication to the wounds so that they would heal in seconds. Temari’s summoning technique, Kirikiri Mai, summons a weasel on a sickle with obvious links to her earlier attack.

2.4 Sandaime’s Nyoubou
This is the stick the monkey god Enma transforms into. In Chinese mythology, Monkey was a young god who went on a journey for immortality. His name was just Monkey, or Sun Wukong in the Chinese, which translates to Son Goku in Japanese (Yeah, believe it or not, Dragonball actually did it’s homework). The Nyoubou was a magical stick given to Monkey by his tutor, and could vary it’s shape and length at will, multiply, transform and had a will of it’s own.

2.5 Tailed beasts
To be honest, I didn’t know of this Legend until recently. Therefore, this will only be a brief overview with links to better explanations. In Japanese legend, there exist 9 tailed beasts, 5 of them being elemental.
One tail - Shukaku - Tanuki/Raccoon dog - God of Wind
Two tails - Nekomata - Cat - God of Darkness
Three tails - Isonade - Horned shark - God of Water
Four tails - Sokou - Half rooster, half snake - God of Poisons.
Five Tails - Houkou - Wolf - God of Illusion, has a tail for each element
Six tails - Raijuu - Weasel - God of Thunder
Seven Tails - Kaku - Badger - God of Earth
Eight tails - Yamata no Orochi - Eight-headed snake - Can summon the sword of Kusanagi (Same as Orochimaru), God of Evil.
Nine Tails - Kyuubi no Youko - Fox - God of Fire.
Each has various intents and purposes, and each won and lost various battles against the other. It is highly likely that the Bijuu we have yet to see will take these forms. Here is a more complete source of information: http://www.inukoproject.com/naruto/bijuu

2.6 Symbols
*Takes a deep breath* Here are all the symbols seen on clothing, ect in Naruto:
- Kimimaro’s red dots on his forehead are a symbol of nobility from the Heian era, called mayu marks.
- Karasu/Crow, Kankuro’s first puppet, has the kanji for “crow” written on it’s chin.
- Kankuro’s face paint is from Kabuki theatre, with purple representing nobility. His robes are black, used to portray a puppet master and a ninja, and the symbol seen on his chest in his first costume contains red for anger, and a sandy colour which probably refers to the desert.
- Gaara’s eyes are dark because, not only is he an insomniac, but the Shukaku inside him is a Tanuki, raccoon dog, known to have dark eye-rings.
- Gaara’s forehead tattoo says “love”.
- The Uchiha symbol is a fan, used because of it’s ties to their family name.
- Sasori means scorpion, hence his stamp on his puppets showing one.
- Medical ninja bear the kanji for “doctor” on their shirts.
- On the front of Zaku’s shirt the kanji for death is repeated three times.
- On the back of Tsunade’s jacket is the kanji for “gambling”.
- Kakashi’s summon dogs wear a face made out of Japanese characters called the “henohenomoheji” (All the characters used to create the face). These faces are usually placed on scarecrows in Japan, which is notable because Kakashi’s name means “scarecrow”.
- The orange toad Jiraiya sometimes summons (The first frog summon he uses) wears a bead stating “loyalty/friendship”.
- The symbol on Jiraiya’s forehead protector means “oil”. Toad oil was thought to have special properties, and sometimes magical ones.
- Gamabunta has the symbol for “shrimp” on his back. Alone this is one of the characters which makes up “toad”, but maybe he just loves seafood? ;)
- On the Yondaime’s long white jacket the kanji on the back spells “Yondaime hokage”.
- Chouji has the kanji for “food” on his front.

2.7 Hand seals
Although the use of hand seals in ninjutsu is entirely made up by Kishimoto, seals are used as ways to focus energy during Buddhist meditation. Also, special hand signs, called mudras, are used to convey a certain concept into the user. For example, a right hand raised with palm facing outwards means “no fear”, and grants the user that concept’s blessing through their meditation. The seals in Naruto are from the oriental zodiac, the 12 animals which name the years (I was born in the year of the snake, for instance), the properties of each seal representing what that animal’s qualities are - Eg, Tora/Tiger seal is fire.

2.8 Puppets
Puppets were long used in Japan as a means of travelling or theater entertainment, the most famous being the Bunraku puppet theater, where large dolls are manipulated using a combination of string and barely-visible poles. Usually the entire body is moveable, including the mouth, eyes, eyelids and fingers. They sometimes contain secret compartments in order to simulate effects later in the play, such as a compartment containing red felt, which falls out like blood when it’s opened. The main dolls usually require about three puppet masters at once, which are usually dressed all in black (like Kankuro) and sometimes hooded. They perform in front of the audience without hiding themselves, as the black symbolises invisibility. Kankuro’s facial makeup is from Kabuki theater, another thing linking his character to traditional entertainment.

2.9 Explosives
Small explosives and smoke bombs were used to distract the enemy and allow for an escape. Sometimes they added metal or sand to make the enemy even more distracted, as shards of metal or grains of sand rip through their eyes. If a large-scale ninja mission was in effect, even though there were many ninja involved more often than not only one ninja had the task of finishing the job, with all the others there just to make a mess and start a panic with explosives and shouts. As for explosive paper tags, that comes from Onmyou, an oriental system of magic, similar to shamanism or western sorcerers. The sorcerer, Onmyouji, enchants paper by writing symbols on it and cutting it like origami (For example, making a paper person and writing your name on it was said to create a double of yourself if you were gifted in Onmyou magic, likewise writing “fire“ will make it explode.) This is similar, and probably partial inspiration to Deidara’s use of clay.

If anyone wishes for me to give evidence for any of this, I can and will happily do so. Also if you want to know more I’ll answer as best as I can. This will be constantly updated as people ask more questions, or I find something worthwhile to add. ^^

Thanks goes to:
-Lalito-, Thetrue4thhokage, Nejishino, Relinquisher, Nonar, Teen_Shinobi123, KanbatsuGaara and Shanigangodzilla for asking questions, and Ichigokenshin369 for helping me answer them. ^^