I pretty much concur with what everyone else has said so far. I have Atari 2600, NES, SNES, Genesis, Gameboy, and Gameboy Advance on my arcade. I find that they all play pretty well. Anything newer than that and it's tough, like we've already covered, because of the 8 ways and limited buttons. Even SNES sometimes it hard for me, just because I have to think of where I have the L and R buttons assigned to, but it's not too bad.
What I do on my machine is that I have two USB NES controllers that I keep inside my control panel. I have my cab configured so that I could either use the normal arcade controls, or else I can pull out the NES controllers and use those instead. I have chairs for my cab, so the standing part is not an issue for me. But some people said it's hard for them to control Mario is Super Mario Bros 3 with arcade controls. I do not find it to be difficult, but I guess others do. I guess when you've played something your whole life on the original controllers, trying to switch to something else is hard for some people. Anyway, I only have NES controllers because that's the system I grew up playing, and it's very near and dear to me. You could have a similar setup for probably any other type of controller, or even all of them if you wanted to.