This guy recommends using FCEUX, which is one of the top Nintendo emulators around. It has command-line support. You'll need to remap some keys.
http://www.flashingblade.net/?page_id=1948His documentation is cool but it's in PDF format. Here's the relevant section for NES emulation, which shows his MameWah config settings.
Nintendo Entertainment System – FCEUX 2.1.0
Switched again to FCEUX and had some wins. Command line is standard and, though it won't work with closemul, the Exit key is mappable to Esc. Get rid of the save state numbered keys (1,2,5,6), so you don't have ugly text popping up every time you press start and you're sorted!
These can all be configured through the GUI.
### 08nintendo.ini (mamewah v1.62) ###
emulator_title Nintendo NES
### List Generation Settings ###
rom_path [emurootpath]\[emuname]\roms
rom_extension nes
dat_file
nms_file [emurootpath]\[emuname]\NES.nms
catver_ini_file
list_generation_method rom_folder
### Execution Settings ###
pre_emulator_app_commandlines
emulator_commandline [emurootpath]\[emuname]\fceux\fceux.exe [rompath]\[name].[romext]"{nodosbox}{safelaunch}
post_emulator_app_commandlines
general_app_commandlines