Well, one of the emulators that he mentioned above (CCS64) was a DOS app until this February...

There were plenty good dosbased emus, as was:
Nesticle, an excellent NESemu, dos based.
BTW, runs also fine in dosbox.....

And before you say most are discontinued, remember that most were fully developed/debugged anyway.

Lots of emulators were DOS programs until they were ported to Windows not so long ago (get outta my lawn damm kids!): For example world famous Mame, Meka, etc. etc.

I've always been partial to WinVice. But I have a HTPC with emu's on it and i use wireless X360 controllers, and usb converted NES controllers and map the emu's to keyboard commands. I use XPadder (http://www.xpadder.com/)for mapping controllers to keyboard layouts which is handsdown the very best utility for joystick and keyboard mappings. I use my X360 analog stick for the mouse too. It's awesome.

The author is on top of his game too. You can even see from the download page where he fixed bugs I reported between releases. I cannot wait to update mine now :)