I've been using Toggl, a webapp, browser-based time-tracking software. And very nice it is too.
But now it comes with a non-free desktop application, which uses a browser wrapper to communicate with your web-based account.
I'm sure we'll see more of this blurring of the boundaries between Free Software and webapps/cloudapps/websites-that-are-really-programs, and it's interesting as always to see what Richard M Stallman has to say about the matter: “The only solution to this problem is not to use someone else's server to do your own computing on your own data. Do it on your own computer, using your own copy of a free program.”