Nestopia seems to crash for me without fail whenever I quit the program in OS X. I am of course using the latest version of the Emu and the latest version of Bannister's Emulation Enhancer, on Tiger.
For what it's worth, I'm tearing apart the shell code at the moment to make it work as a Universal Binary, so I wouldn't worry too much about bugs in the existing version. I'm in the process of implementing a whole new set at the moment!