I've been (heavily) modifying a VBScript I originally downloaded from Lifehacker, at http://lifehacker.com/software/top/geek-to-live--quicklog-your-work-day-189772.php.
The original script just logged your time to a rudimentary Excel spreadsheet. The modifications I've made include:
I run it as a keyboard macro (instructions on how to do that are available on Lifehacker here) and as a Windows scheduled task every 15 minutes (instructions on how to do that are available on Lifehacker here). The most recent modified VBScript is available here. (If you want an old version, email me.) It's freely distributable, licensed under the Free Software Foundation's General Public License. Look at the VBScript to see what to change to have the log files saved where you want (you can edit it with any text editor — right-click on the file once you download it and select "Edit"). You need to change the "filepath" variable, not the filename (the filename never appears in the program text — it's computed from the date).
My original blog post — with a link to full instructions — is here.