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
