I use Filemaker to track time. It's an expensive application, but I've used it to create a Project file, Project list (showing In Progress, Upcoming, On Proof, At Printer, Completed jobs in hierarchical form), Time Sheet, Invoice, and even a quarterly Income/Expense report.
All the lists and forms are related, so when I enter time for a project it updates the total time on that Project, and when I'm done and ready to bill, the Invoice adds all my costs, the printing costs, tax, materials and shipping and is saved to a PDF to send to the client.
Building my own seemed like a good idea because I could never find an app that took all my variables into consideration, and I wanted something custom to my situation as a one-man studio.
But like I said, Filemaker is not cheap, and I spent a fair amount of time learning how to build my Project Management System. In the end it was money and time well spent, but it may be overkill for some.