A Gear motor has a gearbox that increases torque and decreases speed. DC motors might run in the thousands of RPMs, and if you want to do anything slower and with more torque, you need a gearbox (this also works backwards: you could speed up a motor with a gearbox as well, but this drops the torque).
Encoders built in are sometimes great -- you don't need to do any assembly of the encoder + motor. On the flip side, the encoder the manufacturer supplies may be inadequate and you might want to install your own. So it's a toss-up between the two. Although if given the choice, I'd much rather have the manufacturer install the encoder for me...
MIKE