Some people have justified neutering on the grounds that it prevents various diseases from occuring. This is a pathetic excuse to use for justifying neutering for the following reasons:

• There is no guarentee that sex organ specific diseases will occur in an animal (testicular cancer and phantom pregnancies, for instance, aren't particularly common in dogs), and, even if such a disease did occur, there are natural remedies which don't have side effects. Castration and spaying are always last resorts as far as humans are concerned, so there is no reason why they should be used as vaccines for animals (especially for females on the grounds that spaying is major surgery). As millions of years of evolution went into designing every animal, it is foolish to think that removing any part of the animal's anatomy won't result in potentially dangerous side effects from occuring. 
• Neutered animals put on weight quicker then intact animals because of the fact that  gonard removal causes the victim's metabolism to slow down by up to 33%. Other side effects which could occur due to this decrease are constipation, skin and blood- pressure problems, a feeling of coldness and a lack of energy (these side effects are theoretical as far as thier connection with neutering is concerned, but, if obesity can occur due to neutering, there is no reason why other metabolic side effects don't occur).
•  Neutered dogs are also more likely to suffer from from knee ligament degeneration and knee arthritis (which are both expensive to treat, while possibly needing surgery). Neutered female dogs are also quite likely to suffer from urinary incontinance due to the operation (dogs are more affected by neutering then other species as well). As a result of being castrated, some male dogs may need to be groomed more in
  order to stop their fur from getting matted up. In some short coated breeds, the hair may appear to be thinner in places.
• Castrated male animals may suffer from respiratory problems due to the lack of testosterone causing chest narrowing, and spayed females may also suffer from digestive disorders. Neutered humans suffer from a lot of health problems (unless they are given hormone suppliments), and there is no reason why these side effects shouldn't occure in non- humans. Males may suffer from heart disease, strokes, osteoporosis, decreases in bone density and decreases in muscle performance due to low testosterone levels. Females may also suffer from a loss of bone mass and muscle performance, osteoporosis, mood swings and joint problems due to low estrogen levels (there also seems to be a link between estrogen deficiency and Alzheimers disease). The article on this webpage (http://www.healthscout.com/news/1/527160/main.html) contains some useful information about why female humans who have hysterectomies should keep thier ovaries (there is no reason why these findings shouldn't apply to female animals as well).  
•  Both males and females are also more at risk from hypothyroidism (which can cause metabolic slow-down) and cerebellar cortical abiotrophy (which can affect the animal's coordination). There is also a slight risk of a post-surgery infection occuring. This article (http://www.mmilani.com/commentary-200509.html) contains some interesting information concerning cancer and neutering in animals. Also, cancer can be prevented by feeding animals (and humans) foods which are rich in Vitamin B17: http://www.vitaminb17.org/foods.htm contains a list of foods which are high in this nutrient.
•  Here are 2 other other studies concerning the medical side-effects which neutering can cause:

http://www.geocities.com/heartland/prairie/2492/Sexual-hormones.html

http://www.pelagus.net/animal/v02.html

http://www.caninesports.com/SpayNeuter.html