When Appnovation started a few years ago, we did not use any project management tools. We only had a shared folder for managing all the documents associated with each project. Over the past few years, much has changed and we started using a few tools:
1) BaseCamp (www.basecamphq.com)
We use BaseCamp for most our project management. This includes the storage of client contact information, projects tasks, project milestones and project files. We find it to be a really effective tool for storing information. Unfortunately the tool does not have any ticket or bug tracking system.
2) TickSpot (www.tickspot.com)
We use TickSpot for all of our time tracking purposes. The budget feature allows to easily manage the time spent on each project and really figure the projects that we are going over budget on. Before using TickSpot, we were using the time tracking feature on BaseCamp which is not really effective.
3) TRAC TRAC is an open source solution for ticket tracking. It has a really simple interface for adding tickets and associating it with features and project areas. However, it does not have an interface for adding new users. Adding new users require executing server shell commands.
Even though we currently have a great set of tools, we find that it may be time to move on to a more unified system. It is a pain for us to use 3 tools for every Drupal development project. Some tools that we have looked into include: 1) ActiveCollab (www.activecollab.com) This is a tool that combines TRAC, TickSpot and BaseCamp. The amazing part of this tool is that it is highly expandable with a PHP code base that you can build custom extensions with. Please feel free to leave a comment on the tools that you use for managing Drupal projects.