We use Pivotal Tracker for our development management at HUGEcity. It’s an implementation of Scrum methodology which uses an estimated point system to track velocity to enable estimation of complete dates. In essence, “score how I did to predict how I’ll do.”
Because you’re using it to generate time estimates for yourself and, more importantly, for your customer, it’s important to keep it honest. When I see questions on stackoverflow and the like about wanting to apply points to bug fixes I get concerned that the askers don’t fully get what a bug is. To put it simply:
A bug is something that you’ve already spent points on.
A bug is something that you’ve implemented, probably with a point score attached to it that wasn’t really finished. You’ve earned those points inappropriately. Your estimate is off because you actually spent less time finishing the task than your project history says. Leaving bugs pointless pulls your velocity back down to what it actually is.