For SNES emulation, it depends on the game. You have a configuration file for each game. I generally use A and B as A and B, unless for some reason either of those 2 buttons doesn't play a huge role in the game I'm playing... for example, in super mario world, since A does the spinning jump thing and B does the regular jump, I have the Y(SNES) set to B(GP32) and B(SNES) set to A(GP32). That way A and B are used exactly like they would be in any pre-SNES mario game. Then I have A(SNES) set to Select(GP32) because it's closer than start, but still out of the way so I won't do a spin jump by accident. X does the same thing as Y, so that doesn't need to be mapped. I map start to start, L to L, and R to R.
There aren't a lot of games out there on SNES that I know of that use every single button, so it's not a big problem. Even if every button does something, there's always a way to compromise.
With Chrono Trigger, L and R are used to run, pick time periods when you're in the Epoch(D-pad can do that too), and in the squaresoft soft reset thing. So, in conclusion, they're not really needed. A is set to A, and B is set to B. Then Y(SNES) is set to Select(GP32) because it's the closest thing to where Y would be. the X(SNES) is set to Start(GP32). Start and Select(SNES) are set to R and L(GP32). Start is hardly ever used, and Select is only ever used during the soft reset thing. Hmm... Now that I think of it, I might as well put L and R back to L and R rather than Start and Select, since I don't really use either one of them anyway... bah! it doesn't matter, they're all equally useless.