For any workflow, it is worth considering org-mode. It has certainly satisfied me after trying many different alternatives.
It is plain text, so you are not locked into a proprietary object format. Thus, you can edit it using any text editor in case Emacs is not around. In fact, Vim is on its way towards implementing a decent subset of org-mode. GitHub and GitLab also support org-mode syntax and can even render HTML from it. There are also decent mobile clients, and even some bridges to things like Trello.
Emacs has lots of org-mode primitives that can be used to deploy any workflow. Moving items across sections or files can be efficiently done using org-refile. Storing new items on the flight from many different places can be done using org-capture and org-protocol. More importantly, you can easily create alternative views of your files using org-agenda. org-mode also has timestamps, so you can set schedules, deadlines or simply record events.
I've just scratched the surface. My favorite workflow is Ivy Lee's Method, which is a very basic kanban with two states. Easy to implement in org-mode. Just two trees: Today and Inbox. Every morning I refile 6 tasks from Inbox to Today. I keep new thoughts and important items with deadlines, etc inside my Inbox. I can use org-agenda to quickly see if there are any incoming deadlines or events, which I store in a separate calendar file.
If you want to get fancy, you can use lots of trees, one per project. And create lots of tasks to plan things ahead. Then use task states to schedule things for today and get a clean view, again, using org-agenda or a sparse tree. There are infinite possibilities.