JIRA
From APIDesign
JIRA is non-open source bug tracking system. I am not sure why would open source project prefer closed source alternative to open source solutions like bugzilla, but apparently many projects do and use JIRA as their issue tracker.
Few years ago, when NetBeans were migrating away from CollabNet infrastructure, we almost ended up with JIRA, but luckily the decision makers came (were forced to come) to their senses and we are using bugzilla now.