I was wondering this, too, and here's what I came up with: For better or for worse, most of the third-party devs who want to make an epic 3D handheld game make it for the PSP, which is better suited for that type of game.
Of course, Nintendo themselves haven't made a ton of 3D games for it (though they've made a fair amount: I can think of Mario 64, NSMB, Zelda, Nintendogs, Metroid, and Elite Beat Agents/Ouendan). The only other dev that seems to be embracing the DS' relatively powerful 3D engine (and it IS powerful for a handheld, it's just that the PSP is much MORE powerful, making DS look weak).
Square has taken advantage of its' 3D capabilities more than any other dev (possibly including Nintendo themselves), as they have FFIII, Kingdom Hearts, FFIV, V, and VI, ASH, and probably a few other epics either out now or underway that are fully 3D. Also, many of their 2D games feature 3D elements. There are also a few other valiant efforts, such as Brothers in Arms and Call of Duty 4.