I converted my Lion King 3D bluray to my 3DS recently, and my favourite effect is actually from a section where Zazu (the blue bird) flies into the screen, the image actually feels like it pops above the screen for a short period.
In games, there is a brilliant level in Star Fox where the water is rippling, with storm effects and rain, its really visceral and immersive on the 3DS screen...
I'm also in the middle of playing Super Mario Land 3D, and some of the effects have been brilliant.