I primarily use Atari 2600 joysticks with mine. Either originals or a Wico bat-handled one. Sega pads once in a while, but I prefer joysticks.
Original applicable mouse and keyboard all the way. I like my legacy machines to "feel" a certain way. Much of that feeling gets lost when changing out the things you first lay your hands on > input devices. Having said that, I don't require my MacMini running MorphOS to use an Amiga keyboard or mouse although I did hook an old IBM keyboard (the clicky kind) up to the Mini last night for shits and grins. Won't be keeping it on there, mostly because of its size, but I really do prefer white/beige keyboards to this chinsey looking and feeling modern black crap.