As noted in the goldfish thread, it seems like disease is a common reason goldfish or whatever other aquarium fish you have - just don't last. However, though, I'm wondering in more detail, "What exactly are the worst diseases?" and "What are some common ways to protect the fish?". Well, a no-brainer would be an attempt to keep the water as clean as possible.
The best way to protect your fish from not getting a disease is to always make sure that the water is cycled, you are feeding them a top brand food, and that the water parameters are within their range. Always remember that when you add in new fish you should do so by first placing them into a quarantine tank, since they can have diseases that you don't want to get into the main show tank that you may have.
As far as worst diseases, that answer can very greatly by what you are trying to keep. Some are species specific (Neon Tetra Disease, Dwarf Gourami Iridovirus), others only effect a given set of species. Some are more wide spread which can be a bigger pain, if they are common or not treated before they turn deadly.