Guess how long it's been since you last checked the clock
I've found my time-keeping accuracy went up a lot when I started thinking in those terms. I can also often get within 15 minutes of the time by simply estimating how much time I spent on activities since I last checked the clock.
i.e.: "I checked the clock at noon. Then I had to handle that big, complex situation, which probably took an hour. I probably spent ~20 minutes taking a break afterwards so I could be more productive. Then I wrote a couple quick pieces of code, call it 15 minutes each, so 30 minutes. I suppose it's probably 1:50 PM"
This does take a bit more than 5 minutes if I haven't cached anything for a long time, but I can now treat "1:50 PM" as a "checked the clock" and extrapolate off that cached value. Generally I'm only wrong if I've completely forgotten about something else I did ("Oh, right, I had that 30 minute meeting! It's actually 2:20 PM"). Doing this often has gotten me in to the habit of tracking my time, which has the added benefit that I can generally figure out where my time went =)
Recent brainstorming sessions at SIAI (with participants including Anna, Carl, Jasen, Divia, Will, Amy Willey, and Andrew Critch) have started to produce lists of rationality skills that we could potentially try to teach (at Rationality Boot Camp, at Less Wrong meetups, or similar venues). We've also been trying to break those skills down to the 5-second level (step 2) and come up with ideas for exercises that might teach them (step 3) although we haven't actually composed those exercises yet (step 4, where the actual work takes place).
The bulk of this post will mainly go into the comments, which I'll try to keep to the following format: A top-level comment is a major or minor skill to teach; upvote this comment if you think this skill should get priority in teaching. Sub-level comments describe 5-second subskills that go into this skill, and then third-level comments are ideas for exercises which could potentially train that 5-second skill. If anyone actually went to the work of composing a specific exercise people could run through, that would go to the fourth-level of commenting, I guess. For some major practicable arts with a known standard learning format like "Improv" or "Acting", I'll put the exercise at the top and guesses at which skills it might teach below. (And any plain old replies can go at any level.)
I probably won't be able to get to all of what we brainstormed today, so here's a PNG of the Freemind map that I generated during our session.