Aside from not having a PC card slot, the 12" PB also has slower Ethernet (no Gigabit, won't matter if you use only the more widely available 10 and/or 100 MB/sec versions); slower FireWire (one 400 MB/sec port vs. one 400 and one 800, not likely to make a practical difference); and a slower internal graphics card, which won't matter unless you're heavily into role-playing games or other applications that stress the graphics.
The 15" PB can also be bought at 1.5GHz, vs. 1.33 for the 12" and the slower 15". The faster one has a larger disk drive (80 GB vs. 60, which should be adequate for anyone not storing huge amounts of multimedia) and an internally illuminated keyboard, which looks really cool in dark rooms but is IMHO otherwise seldom worth spending real money for.