The best arcade-style controls for retro system are arcade-style controls. O_o
For the SNES and SFC, the Hori Fighting Stick (HSJ-12) is probably one of the better ones, having a clicky stick. It's looser than a Seimitsu joystick and doesn't spring back really quickly, which probably makes it better for fighters and worse for shooters. Works fine on Contra-style games (like Rendering Ranger) though (at least through the run 'n' gun sections). Standard six-button configuration, two rows of three. Some extra features like autofire.
The PC-Engine has a nice-looking stick from ASCII, who made sticks and pads for many other systems too. I have one with a Mega Drive style interface (for the MSX I believe, though it should work elsewhere); joystick sticks on the way back to the center and needs lubrication. Not the strongest spring in the world on that one.
X68000 has a lot of crazy options. Aside from the aforementioned Mega Drive sticks, there's the huge Cyber Stick by Micomsoft which seems more like the shift panel out of a vehicle than a joystick. Probably somewhat cumbersome to use actually. There were also at least two dedicated controllers for X68000 ports of Crazy Climber - I think, would've been dual joysticks right - and a controller made of buttons for Pac-Land (I know this exists, it's right on the game package).
Incidentally, sometimes I like joypads, and sometimes I even like keyboards. I'm not the biggest fan of joysticks, in general, though I have a bunch of 'em.
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