we used harvest at my last place and it was pretty decent. not free but $9/mo isn't bad. and there is also a dashboard widget stopwatch for it as well. it actually was one of the easier time trackers i've used.
creates invoices and has a stop/start clock for each project within the invoice. So If, you have different pay rates, it will calculate them accordingly.
it's a bit over the top, for networked computers in an entire studio... but i didn't pay the pricetag