Cleanliness is important in preventing diseases. If the pathogens are allowed to grow in the enclosure, the animals will infect or reinfect themselves, or cage mates will become infected.
Basic hygienic practices include:
When you have a sick animal, it is a good idea to completely disinfect the entire habitat. Use a fresh bleach solution on all washable surfaces. Other materials can be baked, frozen, microwaved, or replaced to sterilize it. Most substrates should probably just be completely replaced. Live plants are rarely a concern, but they can be set out in sunshine to help disinfect them.
Edited 8-16-2012 (C) Mark Adkins