I use a combination of two methods, one to track the feature requested for project by the "client", one to tracks bugs and tasks.
I used both scumworks and custom excel sheets + white board to track features and their subtasks. Hard to tell which I prefer, I adapt to my team on this. The paper gives more ownership to the team, and excel does the job for the backlog. Scrumworks is a nice a application, nice to manage backlog, display a pretty board that is very intuitive for the team, much faster for the managing stuff (ex: stats), not expensive as well.
I use devtrack, which is a bug tracking system to track everything else. I use this one but many other bugtracking system do the same. Where it becomes interesting is that we use it to track much more than bugs. In one unified system, we track small tasks and bugs, but also art asset integration, audio integration, effects integration, cutscene integration etc. The trick is to have a way to make a custom flow and then a task can travel from one department to another into the predefined order, everything get tracked, nothing is lost, and it is easy for the people because it is centralized. I like devtrack because of the easy user interface, and the control we have over the flow, transition, access, the ability to link tasks into hierarchy. I heard it is quite expensive, but look out for those qualities when choosing a tracking system.
The most important thing is to be able to adapt your tracking method and not get stuck with one when things change. I use a combination of tool, but this change along the project, in the beginning of a project I use almost exclusively agile tracking type, but when closing on to the end, a database with good tracking becomes better for my team. The combination gives us the best of both world, flexibility for what needs it, and strict tracking for everything else.