So we've been using a web-based system called Golaborate to track our work and collaborate with customers on projects for a couple years now. It's built in Drupal and based on packaged installation called Open Atrium. Open Atrium is the best example I know of a Drupal "product" that really gives you pre-configured functionality out of the box. It includes private areas for each project with tools for sharing notes and documents, posting project assets, monitoring project schedule and tracking tasks.
The coolest part is the fact that, like Drupal itself, we can extend it to add whatever functionality we want.
We've added our own "features" to the system to track business development leads and provide a shared company address book. Using common modules in Drupal like Views, we were able to create a feature for global case management that helps our developers get their own work queue and stay on top of things. The global reporting tool also provides us a case scoreboard for knowing how many items are open and what's most important. We built each of the tools in under a day using the framework provided and have been able to refine them over time.
Most recently, we added the TimeTracker module to the system and now we're able to track our time against each individual "case" to know how much time we spend on support on a ticket-by-ticket basis. Next up, we're working on a feature that will capture user stories, otherwise known as our feature list. All of our web projects begin with a strategic engagement where we analyze the project and deliver the "blueprints" for the project including design comps, wireframes and a sitemap. We also create a "feature list" that includes all of the possible things we could build into the site and a fixed price quote for each one. Our clients choose the features they want and then we build the site.
This new Golaborate tool will allow us to create the feature list within the system, empower our clients to approve the features they want and then let us schedule the work into one of our two week development cycles. From there, the options are dizzying. We could automate project scheduling (to a degree), generate delivery calendars, track time against the features, note progress on each feature within comments attached...my head is spinning! (Don't tell my finance folks but we could even automate invoicing and payment through there).
The best part? All within a single system built in Drupal. The fact is that the longer we use Drupal (five years now), the more it keeps proving itself to be just the swiss army knife we need for our projects.