I use a Madcatz Tournament Edition Fightstick for pretty much all my emulation excepting things that require two analogs.
For everything else a wired 360 controller works fine, people bitch about the dpad but that doesn't affect me since I use an arcade stick for anything that uses dpad anyway.
PS: NES Megaman games are infinitely more fun on arcade stick imo, same with really anything prior to psx.