Sim City, the most advanced version the DS technology will allow for (not 4, but possibly 3 and definetly 2000). Loved that game to death on my SNES, and two screens would really help you to figure out what's bothering your citiens with a minimum of lag time switching between graphs and charts. Maybe some sort of amalgamation of the first two games' best features, just as long as they remember to include the Monster and UFO Disasters! 
Seiken Densetsu 3, preferably with extra bosses/classes and Wi-Fi multiplayer.
RPG Maker. Like with Sim City, it probably wouldn't be able to handle the more recent releases (most recent one on the PS2), but the first two incarnations are certainly feasible. Another game custom-made for two screens and stylus use.
Seiken Densetsu 3, preferably with extra bosses/classes and Wi-Fi multiplayer.
RPG Maker. Like with Sim City, it probably wouldn't be able to handle the more recent releases (most recent one on the PS2), but the first two incarnations are certainly feasible. Another game custom-made for two screens and stylus use.