The main concerns aside from parasites and such is from the water quality itself. Watch for signs of stressful behavior such as darting, rapid breathing, lack of appetite, surface gulping and color loss.
Keep careful watch of the ammonia, nitrites, nitrates and pH.
As far as "aquired" problems, white or black spots, white film, lethargy, discoloration as well as some mentioned above.
Have a look >>here
<<. Wetwebmedia has some visual info that might help as well.