It means 'ok' or 'that's fine' - it also sometimes implies a hint of annoyance, but not always. "I don't really fancy eating sushi tonight, I had it yesterday" "Fair enough, how about spaghetti?"

The "hint of annoyance" Cyd mentions is because taken literally, "fair enough" means "I don't think that's 100% fair, but it's fair enough--I'll accept it." That is, "I accept grudgingly." It would depend on the context and the tone of voice. It could also mean sincere acceptance--"I didn't think it was fair, but now the way you've explained it to me it seems fair enough." In that case it could mean "I accept sincerely."