I P2P'd a program called Total Video Converter. It works well and converts anything to anything, from what I can see (well....except flashcart formats). That's what I use to convert Flash vids to AVI to then be converted for my SuperCard miniSD by the SC's movie converter software.
For whatever reason, the Supercard converter seems to like AVI more than MPEG for converting to the SC's preferred vid format, which I believe is GBM/GBS. But TVC will convert to MPEG also. Like I said, it seems to convert anything to anything (except the flashcart formats), even to DVD VOBs. It's a really nice little program. I believe I counted something like 40+ formats it will convert stuff to...and from.
As irpacynot already knows, I have NEVER tried to put a vid on my R4DS. I cram that full of DS games/homebrew instead. So I didn't know how to help him, hence this thread. But I thought I'd mention the conversion program I use in my first conversion step. It's just when it came to converting for the R4DS that I didn't know what to do, just because I had no interest in doing it personally.
This thread will come in handy if I ever decide to try. Maybe one day, I'll actually use Moonshell for something. I've only just sort of booted it once to see it, never actually used it for anything. Is that weird?