Here's how my todo list work. Each project directory has an org mode file named todo-project.org. The org mode file has a current product version todo list and a general todo list. When the current version has been released, its list is moved to the bottom, a new version todo list is added.

The general todo list is for things not fitted in the current version. Its items can be done in parallel to the current release list or moved into the next version list.

The Emacs org mode is just a plain text file and make it very easy to organize the todo list.