The time-track system mentioned in the previous post is not a computer program, but a self-regimen. I selected 3-minute increments because 3 minutes = .05 hours (I like round numbers), and multiples of 3 and 5 are the easiest to memorize and divide.
I looked into Meetimer (since non-work time at the office is by definition time spent surfing the web), and there are probably programs out there that record how much time you spend with a certain program or window in focus, but I decided against them. No computer would be able to log how much time I spent on different projects (teaching, vs three different experiments) and I'm not quite so irrevocably tied to the computer for work anyway.
An actual computer program would defeat half the purpose. In the short term, I want to make sure I'm earning my paycheck, yes; but I also want to make sure some time is being spent on the less pleasant projects, and in the long term, I want to thwart excessive multi-tasking and create some boundaries between work and the rest of my life. This can be difficult; I work at home when I don't need internet access, and play at work when I want to surf the web. Time only counts when I'm watching the clock, so there's a more compelling reason not to fret about research while cooking or shopping.
The Excel spreadsheet gets updated with time spent whenever I stop working, which also lets me see how much time I spend working at a step. Usually this is less than an hour (Go go generation short-attention-span!). Ultimately I hope to train myself toward two or three hours at a time, which will help separate life and work even further. Half an hour of reading followed by half an hour of tv sounds good, but at the end of the day it feels like the entire day was spent working.
If I were really obsessive, I'd buy a stopwatch and carry it around with me everywhere, starting the timer whenever I have a work related thought and stopping it whenever I have a non-work thought. One day we will have chips implanted in our brains that do this for us. In the meantime, it would miss all that experimental design that happens in the shower.
And yes, time spent on this blog counts as work, filed under the general "student" category. I consider it a vital part of my career; if I could vent the frustration or reflect on grad student life, I probably wouldn't have lasted this long.