Shell rot only happens in turtles and tortoises for obvious reasons. (Can you imagine a snake with a shell?)
Both can be painful, in extreme cases they can cause death. Deep rot can easily become dirty and infected. Rot also weakens the immune system making them more susceptible to disease. Even mild rot can cause severe pain, to the point they won't eat, drink, or really move. I've witnessed this with my own turtle.
2 1/2 years ago I took my turtle to the vet because she had some mild mouth rot. They gave her a shot underneath her arm and I bought some medicine for $16 and I still have some left. Her mouth rot came from always being wet (when she eats her food goes everywhere except inside her mouth and she also spends 95% of her time in her water, even in winter.) when I notice her mouth getting a little dry I put medicine on it. I also recently bought VitaShell for turtles or what I call turtle moisturizer. It's made to help dry skin and shell. Every month or so I put it on her shell to help prevent dry rot and I've even used it on her mouth rot, it only cost $5.99 and works extremely well.
Stress and vitamin C deficiency are 2 other common causes of mouth and shell rot. Signs of mouth rot in snakes and lizards include swelling of the mouth. In extreme cases gums will bleed and they can no longer close their mouths. Signs of mouth rot in turtles include a dry, cracked beak "Loss of appetite, Reddened oral tissues, Thick pus and/or dead tissue within the mouth
Drainage from the mouth and nose.
If left untreated, infection can spread from the mouth into the rest of the digestive tract or into the lungs, causing pneumonia."
"If your Turtle's shell is showing signs pitting, soft spots, fluid under the shell plates, discharge or foul smell, or shell plates falling off and exposing tissue, you've got rot" turtles shed their scutes (plates on the back) and only a few at a time. A flaky shell is not the same as shell rot. If a scute comes off and exposes tissue, that's when you have a serious problem.
http://www.wetwebmedia.com/fwsubwebindex/turtshellrot.htm
http://www.petmd.com/reptile/conditions/mouth/c_rp_infectious_stomatitis#.UN1JlXy9KK0
This mouth rot is more on the severe side.
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