Depends on what games you've already played.
There is a Castlevania double pack with Harmony of Dissonance and Aria of Sorrow in one rom.
Drill Dozer is a great platformer with a pretty good challenge to it. Not terribly long, but not super short either.
The Summon Night games are great RPGs.
Final Fantasy 4, 5, and 6 are all really good, and FF 1&2 is also out on the GBA.
Are you going to be playing on a DS? If so, will you have any way to boot slot 2 in DS mode? I just had a crazy idea that might let you have multiple games on the 3-in-1 after all, but only if you can run DS software from it.
Edit: If you're into the whole retro thing, you could put PocketNES or Goomba on there with a bunch of roms packed into the .gba file.