Debating on which and what system to run this on. PC emulation would be convenient, naturally. Is RetroArch running a given core considered a valid emulation mode for submitting runs? If there are specific settings or cores I should run, what would fall under that?

RetroArch is fine. For the core, you would need to use bsnes, higan, or snes9x 1.50 or later.

RetroArch's run-ahead feature, however, is going to be banned for all mega man games since it uses savestates and fast forwarding mid-run.

Yeah, I heard about that feature. I've since Updated my RetroArch builds, but never turned that feature on myself, because it just came off incredibly fishy. Like, how could it know what your inputs would be, you know? Seems like something we'd see in a machine learning timeline, not our current one.

Anything special I should do if I'm capturing from RetroArch?

Run-ahead just rewinds the game X number of frames, puts your input on that frame, then fast forwards back to the appropriate frame. It's a simple concept, but much more taxing on your CPU.

As for capturing RetroArch, these are the rules for emulator submissions to megamanleaderboards.net: http://megamanleaderboards.net/index.php?page=emus

I added a link to the page in the rules here just now since apparently they weren't there before, but they only applies to top level times anyway.

Something like this state load message would suffice:

Although from what I can tell, RetroArch doesn't seem to let you save or load states while it's recording a movie, so it doesn't look like it's possible to make any sort of a tool-assisted movie with it anyway. In that case, if you wanted to be safe you would just have to prove you're playing on RetroArch somehow, such as by showing some sort of emulator message like state-load or framecount, or capturing the entire window.