I haven't had any issues using 3rd party PS1/PS2 pads with a USB adapter on my PC. The only issue I seem to have is an apparent latency from time to time, regardless of whether it's an official pad or a 3rd party pad. It's really only apparent in fighting games, where timing is the difference between a 14-hit Super Combo and a whiffed uppercut. I'm not sure if the other brands are better though...I'm just using a cheapo $10 RadioShack jobber.
I use a DualShock for everything from NES to N64.
NES/Gameboy/Gameboy Advance/Sega Master System/Game Gear: Great, plenty of buttons.
SNES: Awesome, same layout, plus 4 extra buttons (counting the L2, R2, and pushed-in sticks) to assign to functions, such as screen capture. Analog sticks may count as more as well. In analog mode, I mapped the A, B, X, and Y buttons to the right analog stick for some Super Smash TV action.
Genesis: Depends on the game. 3-button games aren't too bad, but when you get to 6-button, even though you've got more than enough buttons, the mapping can be a pain. Using a PS1 arcade stick of some sort or one of the Capcom fighter pads would be a good idea in this case.
PS1: It's exactly what you'd expect.
N64: You'll have more trouble with this than with the Genesis, most likely changing your mappings from game to game. As it is, I mostly only play WWF No Mercy, and the mapping is nowhere near normal. After I sit down with the actual N64, I have to relearn my PC layout. For games like Perfect Dark and Goldeneye, whose control schemes seem like total junk after playing Halo, you could easily map the controls to more closely match those of games with more intuitive controls.
MAME: A great option. You shouldn't run out of buttons and the analog sticks come in handy for some games. I loved to play Night Striker in the arcade and I imported both the Sega CD and PS1 versions, but since they don't support analog control, they lack the full feel. Games like Thunderblade are a bit awkward, as it uses one analog control for throttle and another for directional control, leaving you with the L and R buttons as the only really accessable buttons for firing.