There's a rather thorough total conversion mod called Hack 9, but it's in Japanese.... I'm trying to work through it but it's rather rough going, partly because I have very little time to devote to it.
Some comments about it over at AGTP's board, where I first read about it: http://agtp.romhack.net/pantheon/index.php?topic=210.0
Anyone else have any experience with this one, particularly on how to get anything that uses MP?
Sometimes interesting things get uploaded here. http://doukutsu.bex.jp/ Pretty much everything is in Japanese though... ...and on a side note, I'm pretty sure that Hack 9 was made from scratch, and not a mod of Cave Story. I could be wrong though.