bperrybap:
There are also some hardware kludges that involving adding a cap or resistor (depends on which board you have) that can disable the auto-reset in hardware.Google around for Arduino disable auto reset, and you will find information on how to do it.
Cutting the "reset-en" trace is probably the simplest (and reversible) way of disabling auto-reset. I'm not sure when this was introduced, but the current Uno and Mega both have this (nice) feature.