I have one of each (300mhz clamshell, 12" 600mhz dualie). The battery life is pretty similar, though a clamshell may get slightly more (depending on specific model, age of the battery, etc). OSX currently gets less battery life than OS9, but it is improving. UNIX doesn't have any built-in battery management, but Apple's doing a good job. Panther should see even more battery improvements.
I think the size, weight, additional USB port, Firewire (not available on all clamshell models) and, most importantly, the higher screen resolution of the Dual USB models makes them a HUGE favorite over the clamshells, in my opinion. The battery difference is pretty negligible, and the other advantages of the Dual USBs far outweighs that.
Don't get me wrong, I love my clamshell, but the little white wonder is light years ahead of it.