What I most expect with 3DS hacking is GBA and SNES emulators.
Although it wasn't perfect, playing SNES on PSP was so amazing, although it couldn't handle ports of the most recent versions of snes9x, since 3DS is quite more powerful than PSP,
I hope it can handle it. But anyway, if it get's as good as PSP's SNES emulation I'll be happy.
Since GBA has a somewhat different aspect ratio, it doesn't get fullscreen on DS, and if you also play a GBA emulator on a DS flashcard on 3DS, you'll be limited to a very small part of
the screen. If we get a GBA emulator working in 3DS mode it can use the top screen, wich is 16:9, making it possible to use most of the screen.
It will also be possible to zoom it to 16:9 ratio losing very few of the original image.
It would be also possible to simulate a cable link and play multiplayer games wireless.
There are some games lke pokémon that would benefit from the 3DS clock, having a day-night cycle working properly.