So it turns out the 3DS can transfer some DSiWare (read: most) from your DSi. I thought I'd take a sec to explain the process to anyone else who might be in the same situation.
1. Download the transfer tool from the DSiWare store (on your DSi).
2. Open the transfer tool.
3. On your 3DS, go to Settings->Other->System Transfer.
4. Follow the instructions. Your 3DS should be waiting for your DSi
5. On your DSi you can choose what to transfer
6. Select what you'd like and accept the transfer on the 3DS
7. Wait for the transfer to complete. Goto 6 if there are more things to transfer.
You can transfer everything, or customize the transfer. I transferred just the DSiWare games I had. Turns out that save data doesn't transfer over though... which kinda sucks. Also there is no way to mass-transfer all of the DSiWare software at once. You have to transfer each title individually. Still, the process was very smooth.