I recently played all the way through Final Fantasy 2j (unofficial english translation) using Nestopia v1.40 on a desktop computer running Windows 7 Ultimate. Didn't experience a single crash.

Unfortunately, I have to agree with the suggestion that the problem is likely the computer and not the emulator itself.

EDIT:

I'd recommend running some hardware diagnostics:

http://www.mersenne.org/freesoft/

http://www.memtest.org/