Hooooo boy, there's quite a lot to recommend...
Doukutsu Randamu is the first thing that pops in my mind. Calling it a Cave Story mod feels a bit disingenuous, though, as it's basically a whole dang roguelike using the Cave Story engine as a base. The levels are randomly generated, and there are a
ton of items and characters available to use.
Does Not Commute is a pretty funny, short (I think) mod where you have to guide a variety of Cave Story characters to their destinations, all the while avoiding the movements of the characters that you previously controlled. I
promise, that explanation will make a lot more sense once you get into the meat of the mod.
Sunset Challenge is a difficult mod in the vein of the CS+ challenges, but also a very pretty mod. Again, short and sweet.
If you're looking for an adventure that takes place before or after the plot of Cave Story, I'd say
Evergreen (a prequel) and
Another Cave Story Sequel will satisfy in that regard. Both are a little more story-heavy than the original Cave Story, but they also have some interesting additions in the gameplay department that help give them their own identity.
The "This Mod Makes No Sense" Trilogy (
Original,
Jack's Bogus Adventure, and
Twice upon Itoh) are filled with completely bizarre gimmicks that are pretty entertaining to experience, I think. Just beware: this mod has EXTREMELY dumb humor. Like, barely beneath
Cavern Tale levels of dumb. That may be a turn-off or a turn-on, depending on your sense of humor. (I am one of those people)
Test your Cave Story know-how in
The 2000 IQ Cave Story Quiz! At least... if you think you're ready. Truth be told, some of the questions can get
quite devious...
You'll notice I haven't mentioned a lot of older mods, and that's because, truth be told, most of the ones I'm aware of aren't... that good?
WTF Story starts out kind of strong, but devolves into weird gimmicks and fetch quests by the end, and I'm sure you've heard the horror stories about
Jenka's Nightmare's unfair puzzles already. The only "old" Cave Story mod I'd wholeheartedly recommend is
Rave Story, which I feel has aged gracefully compared to others of its ilk.
Aaaaaaand once you're done with the whole list I've given you, don't forget to check out
Doukutsu Club for all of your Cave Story modding needs!