The Crowned Witch -> SP's very own mod, good length so far, hasn't been updated for a while though.
Eternal Chaos -> ZT's big chapter-based mod, dunno if it's still available on the forums, but he gives links in the (dead) chatroom.
Corridor/Corridor2/Heaven's Tower -> Speed-/perfection-play style mods, the former two are HARD and by Softmints, latter is by ZT. Mostly finished I think.
Julian's King -> Softmint's mod. Is hard. Pretty dead, but he showed up a while ago and said he might work on it IIRC.
Legacy Story -> Nator's hyped but abandoned mod. Short, only a coupla levels.
Magic~ -> Metalogz' surprise mod, has some good content, maybe abandoned?
SeriousFace's Hard Mod -> A working over of the original CS, complete I think, in the "Want to play my edited game?" thread. Very oldschool forum mod.
The Wrath of Rafflewashery -> Wedge of Cheese's mod, new but pretty big. Features new music
The Zealous Caves -> Don't remember much about this one, think it's a re-doing of Cave Story with a different character, but from what I remember it's pretty good. Short, possibly abandoned.
There are just some, don't get mad I me if I didn't mention any specific ones not already mentioned, it's late and I was looking for ones with some content >_>