For collaborative stuff, we (being myself and my main client's company) use Leankit (
Lean for Business | LeanKit) to track projects via a Kanban board. Truth be told, I don't know what half the columns or sections even refer to. We also use Slack for collaborative chats, but it's painful having to type everything out s now we have a conference call every morning where we discuss a project.
For my own projects I just have a whiteboard on the wall by my desk. I use it to track time on jobs, deadlines, what needs invoicing, upcoming, work, hell it even serves as an eco-friendly sketch pad for jotting down and refining ideas. I use FreeAgent for tracking my finances and it also allows me to set up jobs, create estimates, track time, etc, but it's so much more effort to do that than just write it down. When I (rarely) work for another agency in-house as a freelancer, I keep an A4 timesheet on my desk and just track my hours for whatever project I'm on throughout the day.
I find a lot of 'productivity' tools are just fancy distractions. They're certainly useful when you're managing larger projects, but for me there's nothing quite as satisfying as scrunching up that last post-it note and finishing for the day.