I would say that the number one disease that I tend to see in other fish tanks (the stores, friends, or even those in groups) is Ich. Without a doubt it seems to be the most common, followed up by popeye for some odd reason.
Now after having a good experience in aquarium, i don't run into diseases now. But during my early days would often get white spots, fungal infections and fin rot. Now am free from these headaches. You can easily avoid these diseases by keeping a separate fish tank where you will put new fishes that you buy from the aquarium and observe them for a week before introducing them into your main tank.
Ich would have to be one disease I find many always run into when it comes to keeping freshwater fish. Friends as well that I have who own freshwater fish have nearly always complained of their fish getting ich more so than any other disease I have heard them mention.