Be careful not to put fan games and indie games in the same basket.
Ah, yes, that is true.
I would probably allow the original PC version of Cave Story if someone were to map it. (Why haven't I played this yet?) The game has since been ported to DSiWare and WiiWare, which certainly helps.
But I wouldn't put up hacks and mods. I've dabbled in RPG Maker long ago myself, but while it was interesting (at least for experimenting on my own, I rarely bothered to even try others' games), I'm not opening that can of worms by hosting that sort of thing. As I said, I should go over the PC section carefully, because I may already have stuff there that doesn't fit my criteria.
But hey, if you want to run your own map site and have maps of hacks/mods/fan games/etc., go right ahead.
Because of shareware (back in the day) and downloadable games, it's unfortunate I can't just say the game has to be a boxed game to qualify...