For me: Flagyll is used to treat giardia (protozoa). Giardia is a nasty little bug that is generally either passed by eating other animals who have it or by drinking water that is not sterile. It is not just a reptile parasite, but can also be gotten by humans. In reptiles it makes them refuse food, dehydrate, and regurgitate. I hear from a traveling friend it does about the same for humans.
The last animal that I had with giardia was a leopard gecko bought at a show. Thankfully I quarantine religiously so while I lost the animal no other animals (or me) caught it. I swear I force fed that poor little guy for 2 months before he passed on.