Here is my top 10, but note I'm still working on a few big games. I only touched DQIX and Golden Sun, so they could very well come strong on my list.
1. Advance Wars: Dual Strike
2. Fire Emblem: Shadow Dragon
3. Pokemon HeartGold/SoulSilver
4. Pokemon Black/White
5. Front Mission
6. Picross DS
7. Advance Wars: Days of Ruin
8. Super Mario 64 DS
9. Planet Puzzle League
10. Final Fantasy Tactics A2
On my TDL (I have a few cause I actually only play my DS when I'm out) finish Front Mission, HeartGold, DQIX, Golden Sun, Suikoden, and by this point I should get a 3DS, but If not, Knights in the Nightmare.
Edit: I didn't put Chrono Trigger on, but thats because I beat it as a SNES game, and look at it as a console experience. If it had to go on this list, it should go on top because Chrono Trigger is my favorite game, but actually I'd put it just above Front Mission because #1-4 are games designed to be played on the hardheld, and are very fun even in the 15 minute bursts I get to play them. CT and Front Mission are longer, more in depth games which are better on console (but FM isn't bad on handhelds as it is mission based).