Not counting or repeating series here, just individual games. Also, not including ports or Chrono Trigger would definitely be my favorite game on the DS.
Makes My Top 30 Games of All Time:
1. Phoenix Wright: Trials and Tribulations (+ all other AA games) - Extremely deep story and character development, and sharp exposition.
2. Professor Layton and the Unwound Future (+ all the Layton games) - Very well made story, interesting yet difficult puzzles, and gorgeous art style.
3. Elite Beat Agents - Wacky, zany, hilarious, addictive, and very retro yet accessible song choices.
The Rest:
4. Pokemon Black and White 2 (+ all other Pokemon games) - The deepest and most developed Pokemon game thus far in the entire series.
5. The World Ends With You - Brilliant story, cool art style, well made urban environment and interesting gameplay concepts.
And the Rest of My Top 10:
6. Ghost Trick - Great story and incredibly fun and unique gameplay.
7. Radiant Historia - Perhaps the best non-Pokemon turn based RPG on the DS, and one of it's later gems.
8. Grand Theft Auto: Chinatown Wars - The most intuitive version of this game available is just as good as the bigger GTA titles.
9. Shin Megami Tensei: Devil Survivor (+ SMT: DS 2) - Deep and rich gameplay with a dark yet fascinating storyline.
10. Advance Wars: Dual Strike & Final Fantasy XII: Revnant Wings - Both have immersive SRPG gameplay and storylines that tie in well with their predecessors
Runner Up That Must Be Mentioned:
11. Bangai-O Spirits - I have sunk in so much time into this game in taxis and long trips that I can't not mention how awesome it is.