Back when I was on Windows (Went 100% linux about a 18 months ago), I had one favorite tool that I still miss to this day called TimeSnapper [1]. The underlying concept is pretty simple. It takes a screenshot every x seconds, allowing you to track and play back everything you do on your computer. It also allows you to filter the time spent on tasks according to app titles and browser URLs.
I used it to track my time on client work for a couple years. After a couple weeks of playing back my day and adjusting the filters, I found it to be fairly accurate in tracking what I was doing at any point in the day - including tracking how much time I slacked off or researched subjects and so-on. The passive nature of the tool along with the filters and timeline made it one of the most useful time tracking tools I've ever used.
I have no affiliation with the app or developer besides being a satisfied customer.
1: http://timesnapper.com/
