Mess runs nes really well. try it out. You will find that Mess can do many of your rom collections.
Commandline : nes -cart "%path%\%rom%.%ext%"
Executable: C:\101\mess\mess.exe (or what ever your path to mess are.
Install Mess and all the roms (system roms for mess not the nes roms) in one folder. In the mess folder there is a folder called roms. Here you need the system roms. One for each system you want to run. Get the whole collection compatible with the mess version you get hold of.
Rom extention is 'nes' in my setup. Dont know if 'zip' works. Otherwise unzip your nes collection.
For SNES i use snes9x since it can quit by esc button and runs all games. and it can be fully custoized for buttons and have a nice video quality option with plenty of filers to select from. I recomend it.
Executable: C:\101\snes9x-1.51-win32\snes9x.exe (edit to your path)
Commandline "%path%\%rom%.%ext%" -esc (i dont remember if you need to edit the snes9x ini file to get it to respond to 'esc' button, or if the line in commandline does the trick.
Try it out and find all the systems that mess emulator can run for you. Colecovision, intellivison, atari 2600/5200/7800 and some sega's and more..
Good luck, Henrik