I use GitHub issues and labels. Every issue starts out with a backlog label, when I pull it off the backlog, I assign it to a team member, add in-progress label

I use GitHub issues and labels. Every issue starts out with a backlog label, when I pull it off the backlog, I assign it to a team member, add in-progress label, and the assigned member will go through it and apply an estimate label saying how long they think it'll take to do. When they're finished, they'll submit a pull request mentioning the issue, and apply a spent label signifying how long it actually took them. All issues also get scope and type labels. Type signifying bug, feature, hotfix, etc. Scope saying what piece of the software it's for. We also use milestones for releases. Each release gets a codename, and that codename is used for the milestone and all backlog and in-progress issues are applied to the release it's meant for. Right now there's no UI for anything, but we're building internal tools that create a visual of this whole system for us.