Mednafen is a pretty good multisystem emulator. Nestopia is also decent.
By the way, if you want to try MESS, use -nonu to turn off the "new gui" and see how that goes with you. Also, keep in mind that any settings you set with the MESSGUI.EXE for a system are saved to INI so you don't have to use commandline switches or such. Just turn off the new ui and set fullscreen on anything you want to use with the front end, and you'll see nothing resembling windows.