We've written before about our workflow, and the tools that we use, but one thing that I've also missed from my Fogbugz days is the link between issues and commits. We've tried various methods, including adding branch names to Trello cards to try and link things together, but it never really caught on as it required more attention to process detail than most developers can cope with.
The good news is that we seem to have solved the problem, and the solution (h/t @stevejalim) could not have been more obvious, or simple. Instead of creating a new branch, and then backfilling the related Trello card with the branch name, simply use the Trello card ID as the branch prefix. Not only does this link the two together, but it enforces a critical part of the workflow - having a Trello card before you create a new branch. This prevents the ad hoc "I've just got ten minutes between tasks, I'll fix that thing that nobody knows about" branch, and ensures that everything is documented.