From an Agile process standpoint, issue trackers are used to help with the minutiae and details of the Agile process. The entities handled by the issue tracker might represent work items, bugs, and issues. Most Agile processes include an idea of how to manage tasks that an Agile team are to perform, in the form of Post-it notes on a board or an electronic equivalent.
When working in an Agile setting, it is common to have a board with issues on handwritten Post-it notes. This is a central concept in the Kanban method, since Kanban actually means signboard in Japanese. The board gives a nice overview of the work in progress and is pretty easy to manage because you just move the Post-it notes around on the board to represent state changes in the workflow.
It is also pretty easy to change your Kanban board by just rewriting the various markers, such as lanes, that you have written on your board:
Physical boards are also common with Scrum teams.