No love for Lock's Quest? I haven't played many games on the DS this year, but here's my list:
1) Dragon Quest IV
2) Lock's Quest
3) Final Fantasy IV
Oh, and I wouldn't argue with the inclusion of Professor Layton in any "Best Of" list. In fact, it might bump FF IV off my list - it would be close.
Note that I haven't played TWEWY or Chrono Trigger, though I bought both when they came out...