I like the ideas mentioned so far but, I will throw my list in the mix. Some of it has been mentioned.
1)RTC
2)lipo battery charger circuit/ out-put booster
3)micro SD slot
4) adjustable level shifter for serial out. I want to talk to inverted serial at 12 volts/0 volt personally but, also talk to 3volt and 5volt levels that Arduino uses.
5) It would be nice to have a inline pin-out for LCD or GLCD screen. Basically, 20 pins in a row that wires could be soldered into.
I will keep thinking.