I used FCEUx for a research project. Fair warning I've only ever run Super Mario Bros and Duck Hunt on it, but it's pretty intuitive and should work with any NES ROM.
FCEUX is the best NES emulator there is. Emulator Games and ROMS Forever are the best sites for downloading ROMs.
That's probably either due to two reasons then.
(1) Your computers processor isn't up to par. (2) The Emulator isn't programmed well enough to make proper use of your processor.
Emulation generally requires around 10x the processing power of the original system, so yeahhh. I'd look into a different emulator and see if it's more stable.
http://fceux.com/web/home.html
Give that emulator a try.
download fceux
find some roms
get a classic NES USB gamepad
nostalgiabate