I found one of the new six-button USB Genesis pads being sold in a store (regional chain called The Exchange) so I bought it and hooked it up to my PC. Tried to play the Genesis Classics on Steam and it's been a frustrating experience.
Firstly, you apparently have to hold the Start button down for five seconds to switch it to X-input (it seems to default to D-input). Even after doing that, it won't recognize up and down on my D-pad. Nothing happens when I press up or down. Left and right work fine, though.
The buttons aren't mapped the way you'd think, either. I had to go into the Genesis Classics configuration to remap the C button (it thinks the pad's C button is a left bumper button on an Xbox controller) and the Z button (which it thinks is an Xbox right bumper button). So that was annoying.
I still have no idea how to fix this D-pad issue. Trying to map individual D-pad directions doesn't work because the Genesis Classics config acts like you're pressing nothing.
[edit] I tweeted with Retro-bit and they helped me out. I moved the controller from one of my front USB ports to a rear port. I also rebooted and then held Start for five seconds to switch to X-input before starting up Steam. Now everything works fine in the Sega Genesis Classics collection as well as in a couple other Steam games I tried out (Shantae and the Pirate's Curse and King of Fighters 98 UM).
Metal Slug in Steam was acting weird, though; couldn't look up for more than a second before my guy would go back to pointing horizontally. I don't think the game is supposed to work like that.
Anyway, I tried to plug the controller into my Xbox 360 but it didn't work, even after holding down Start.
Plugged it into my PS3 and it worked right away, happily. Didn't have to hold Start. Tried out Bomberman '94 and it performed just fine.