- Fogbugz
- Unfuddle
- Pivotal Tracker
- Bugzilla
- Redmine
- JIRA
- Linear
- Basecamp
- Spreadsheet
- GitHub Issues
- Codetree (I ran this)
- Zenhub
- Shortcut
Probably missing a few. I've settled on Shortcut for now (formerly Clubhouse). It's a good balance between the "bag of bolts" JIRA approach and the "one way to do things" take that Pivotal Tracker has. Shortcut gives you sane defaults but with enough customization to suit reasonable workflows.
One trend that I don't really get is dev teams using general purpose tools like Trello or Asana to run their software projects. Sure, it's possible to do. But I find it much more sensible to use a purpose-built tool that understands the kinds of first-class objects (Issues, PRs, Comments, Workflows, Workflow Stages, Tasks). Makes life a lot easier.