I am a project manager for a small digital solutions team within a publishing organization.
We use Trello to manage our app/website projects from contract signing to store publishing and beyond. While we've changed our systems many times over the last 5 years, one thing has remained constant - the use of Trello!
Currently, we have a board that manages all of our incoming/ongoing issues, one for our developers to sync work to from Github and manage releases and one as a resource/reference library. Labels help with being able to filter to a specific project at any given moment. We also heavily use Butler for automation (and we've been through all of those expansions too).
My biggest tips with using Trello are: