I'm surprised GitHub is by far #1. I wonder if it's familiarity rather than preference. Github's minimal approach of using labels for everything is like Gmail's tags over folders. I wish GitHub had a "This bug affects me" or +1 button so the comment history stays clean of "me too" responses.
I've used a ton of bugtrackers, GitHub is the only one I've been able to hand to a non-techy client so they can create bugs. This has been a huge frustration for me when it comes to bug tracking. I have multiple clients who just aren't technical people and when they see the wall of options that bugzilla and mantis offer it causes them to give up and email me directly. I even tried vbulletin for awhile, but that had i…
I was using Pivotal Tracker a few years ago for a large-ish project, and really wanted the client to use it.
It didn't strike me as terribly hard for reasonably bright people, but I under-estimated habit and the degree of resentment some members on the client team had about their pet project being changed.
Assorted attempts at education (I made a really nice screencast!) failed; I was still getting e-mail with Excel or Word docs attached.
We finally came to an understanding and started using Google Docs.
BTW, Github issues is not so bad. A key feature for me for any bug tracker is a Web API, something I can talk to using a command-line tool.
I wrote such a thing for Pivotal Tracker (my Pivotal Slacker Ruby script, now abandoned) and later hacked up a program called GHissues to pull items from Github.