So, I did some learnin' on thermal design. I modified the PIPduino design to use a different regulator. The board has thermal vias that dump heat into the top ground plane as well as the bottom and fairly wide expanses of copper on the bottom. It seems to work pretty well.
I ran the regulator above it's maximum rating (9.7 ohm, 5.05V, 520mA) for five minutes with a Vdo > 7V. The hottest spot I could find was 140C (ambient of 22C) and it stayed stable at that temperature. At ~250mA for 5 min the hottest spot was around 92C. I can probably further improve in the next revision.
Just don't touch the board. It's hotter than the devil's ass on fire under these conditions.