We used molex-type connectors last year. For lower current spikes and motors we used AMP Universal MATE-N-LOK Connectors. These are rated for up to 15 amps and accept 14 - 20 AWG or 18 -24 AWG wires, depending on which contacts you buy.
For the higher current PWMs and drive motors, we used Molex Mini-Fit Sr. Connectors. I believe these were rated for either 30 or 50 amps. The contacts accept 8 - 12 AWG wires.
Unlike the battery connectors, these both mechanically lock to their mating connector so they can't vibrate loose.
They are available from Mouser.com -- see the following pages for details:
http://www.mouser.com/catalog/620/868.pdf
http://www.mouser.com/catalog/620/898.pdf
--Ross