Match the pad to the console library you're emulating.
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Emulation quality on PC is mostly solved; the controller is what is usually holding the experience back. A mushy modern D-pad makes 2D platformers and fighters feel wrong no matter how accurate the emulator is.
Pick the shape that matches what you play most — there is no single best pad across all eras.
A crisp cross D-pad and two-to-six face buttons is exactly what NES, SNES and Genesis games were designed around.
3D-era games need real analogue input. A standard wireless pad is the practical choice, or a dedicated N64-style pad if you want the original layout.
Arcade ports and 2D fighters were built for a lever and a button cluster. Nothing else feels right for them.
Classic look with modern sticks and triggers, so one controller covers both the 2D and 3D shelves.
A classic rectangular pad with a genuine cross D-pad. Modern analogue-first controllers make precise 2D platforming harder than it should be.
Wired or a 2.4G dongle keeps latency lowest. Bluetooth is fine for turn-based and slower games.
Only if you want the original feel. Any modern pad with an analogue stick plays N64 games well, and often better.