Shell Rot
What it looks like: White or grey spots on your turtle's shell that actually penetrate the outer layer of the shell. The area may be soft. Really bad cases have a rotten smell, are soft, weep, and are red and bloody.
What causes it: Generally unclean water conditions. It's usually a bacterial infection that starts from a minor cut or scrape or from a fungus left on the shell too long, but can start by itself.
How can I avoid it?: Keep that water clean! I know it's hard. Hey I had to find out the hard way so hopefully I'll save you and your turtle some greive, pain, and expense. Use water tester kits (get at a pet store) and test pH (should be between 6.5 and 7), ammonia and nitrate(should be 0), and nitrite (lower the better, hard to do). Take a look at the What You Need section of the site for ideas on keeping the water clean.
Keep a close eye on your turtle. Examine it and occasionally take it out of the water and let it dry out completely for a couple of hours. Bahamut had some small soft spots on his plastron that I only found after he dried out. Be sure to check the plastron too!
Provide a basking area. I know, they rarely use it but provide it just in case. If your turtle never uses be sure to force it to dry out as I mentioned above
How to fix it: This can be very difficult and can take months. Your best bet is to never let the conditions get right for it to occur.
If it does crop up, how you proceed will depend on how advanced the shell rot is but all involve immediatly cleaning up the tank and fixing whatever problems your system has to let this occur. If you don't do this your turtle will never get better.
Small white spots, not deep, no drainage, no smell, still firm:
Great, you caught it early, the second best you could hope for. Using a damp towl covering your thumb, gently (but firmly) wipe over the area a few times, trying to remove the white pit. If that doesn't work try using a blunt plastic tool to carefully try to scrape the white pit off the sore. Don't use anything sharp, press too hard, or try too much (just a few times). If it doesn't come off relatively easy now it will soften after some treatment, maybe a few days..
You now need to treat the spot(s). Their are several medications that are recommened but one that I've used succesfully and comes with lots of good recommendations is called Nolvasan (see below). That's a brand name of Chlorhexidine diacetate, there are generic versions available but I stick with the brand name. One of the other commonly recommended medications for this treatment is Betadine (see below). It's sort of fallen out of graces of some reptile folks because if over used it can quickly become toxic but I like to use it sparingly and alternate using it with Nolvasan.
Gently, clean your turtle all over with a soft toothbrush to remove any algae, fungus, dirt, and help remove shedding skin. Rinse and dry. Use a cotton swab (what? no brand name??) to apply a thin coating of the chosen medication to the affected area.
Don't over do it! More isn't better. Remember these guys are pretty small and too much medication can become toxic. While both Nolvasan and Betadine are pretty gentle (Drs pour it on trama victims like water) too much can lead toxic poisoning and even organ failure.
Let your turtle dry out completely for 2-4 hours. Get a nice sized plastic storage container (Rubbermaid, Sterilite) that is big enough so your turtle has some moving around room and can't escape. Line it with towels (just make sure your turtle is dry before you put it in or the towels will stay damp) and put it in a quite, secluded, dark area. Be sure not to forget about your snapper though! Also you don't want it to be to cool or hot, normal room temps in the low to mid 70s F.
You're going to want to keep this up daily until the sores heal. If the pit didn't come out keep trying each day or so. I've found that they come out best when the turtle is wet so try when you 1st pull your turtle out of the water to begin the treatment.
Some options that I've read/heard/tried:
You can try using an antibiotic ointment over the area. Use a water based ointment that will dry (prescription Silvadene cream is great) and not keep the area moist is what you want. Just apply a very thin layer after the liquid medications.
Try alternating between Nolvasan one week and Betadine the next. I've read that Betadine can actually slow the rate of shell regrown on the affected area so I only use it early on, stopping after the pit comes out and using Nolvasan exclusively.