When in the GBA mode of the DS, there is no way to access the wifi hardware, and the link cable parts of the motherboard have been crippled beyond repair. The short answer is no.
However, NES DS apparently has a multiplayer mode that may work if you have the right version. That's really the only emulator I've heard of that has that feature.
EDIT: Lumstar, you are correct. The timing of the serial-based link cable was very difficult to program for, even among official developers. The only programs I can think of off the top of my head that managed to program around those limitations are PocketNES and Herg's Solitaire.