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