I use the Trinity Reference cells. They fit in the battery compartment a lot better than the stock batteries and have room to spare for the wires and connectors. You can get them at Tower Hobbies [a sponsor of this site]. They have up to 4600 mAh, but I am using the 3000 mAh and run time is well over an hour. I've never had it die on me in a single session...
http://www3.towerhobbies.com/cgi-bin...?&I=LXTAT5&P=7
If you order any battery online, watch to not get the Traxxas connector models...