preamble
It seems to me that computer programmers are one of a select few groups of people who actually take pleasure from sitting in front of computers for long periods of time. Most people in other professions actively dislike their time at computers, and do their best to avoid it (so, I assume, they don't have problems taking breaks). At least for me, having external cues for taking breaks, and clear instructions on what to do with each break (stretch, go for a walk, close my eyes, look into a distance of preferably a few km and focus on faraway objects, etc...), is a must.
So far, I've just been making up the breaks and tools to get them as I go along, based on what looks to be low-specificity information found on the net (generic stuff ala ergonomics advice for office staff). This has led to all sorts of side effects - loss of attention as I get distracted if I walk around, breaks in flow with alarm clocks interrupting my thoughts, and people around me assuming I'm low on work due to the frequency of my walking around compared to everyone else.
/preamble
tl;dr
Taking breaks is important
My internal break taking system doesn't work, and ad-hoc ones have unwanted side effects
What do you do to make sure you take proper breaks?
How do you avoid unwanted side-effects, such as getting distracted or interrupting flow or giving your co-workers the impression you're spending a lot of time goofing off?