I use a Kanban (or GTD, depending)-style workflow using Org mode and Gnus. Org mode recognizes `gnus:'-prefixed links. For certain types of mail, I use an Org capture template within Gnus which inserts a TODO item into an Org document, along with a link to the original message (which can be opened in Gnus using C-c C-o).
You can then go through your usual workflow as you would with any other item; mail is just another source of data.
Considering that the task originated via mail, chances are it'll require some back-and-forth, potentially over the course of weeks and perhaps with a handful of people involved. I also keep detailed timestamped logs of correspondence and my actions, linking to important messages as needed. This is particularly useful for large threads, since I highlight the most important information. Since I'm logging via Org mode (and not my MUA), my logs can also include any other additional information and time tracking that has nothing to do with mail, so this creates a useful timeline that combines both actions and correspondence into a single view.
Because this is married with the rest of my Org-based task management, my mail also shows up in my agenda and reporting.