I've just got a 5D2 with micro-adjustment for the first time. Basically, I think I'm going to leave it alone! It's difficult...
The main problem I've had is that with all my lenses being f/4 max, even on full frame there's quite a lot of depth of field if you test at sensible distances (Canon recommends 50x focal length) and tiny focus shifts are hard to estimate. You could also say that therefore any discrepencies are less significant (which is true) but that's not the point of playing with it! (On a 50D, DoF at f/2.8 will be roughly equivalent to f/4 on full frame.)
Anyway, after an hour or so of fiddling, I set my 24-105L to +5 and it was spot on every time at 60mm. Each increment of 5 was shifting the focus point less than one inch from 10ft or so, which I think is incredibly fine for the focal length and likely real world subjects. I could detect shifts in increments of about 2-3 reasonably well, but you have to look damn hard.
Then I tried my 70-200L 4 IS and settled on +4 at 70mm, again at 10ft distance. I was nearly blind by this stage. Then without changing distance (kind of typical long-ish portrait range I thought, so therefore valid) I zoomed it to 150mm and then it needed to go back to zero, maybe a touch of minus!
I had a go with the 17-40L but it was impossible to see any shifts at all with that except at silly-close distance.
I then gave up and reset everything to zero, in the fairly confident knowledge that the factory calibration is probably as close to the best average setting, at different focal lengths and focusing distances, and that whatever discrepencies there may be are insignificant compared to all the other variables.
I need to do some more tests, mainly out of interest, but the point I want to make is that a) it's difficult, and b) there are real changes when you alter focal length and shooting distance. The obvious corollary is that if you yield to temptation and optimise it for an unrealistically close shooting distance (so you get shallow enough DoF to see the changes), or don't check the full zoom range, then you're quite likely to make things worse for a lot of real world shooting.
Canon's recommended test procedure is here, from Chuck Westfall, second question down
http://www.digitaljournalist.org/issue0812/tech-tips.html
Edit: If this comes across as saying micro adjust isn't necessary and best left alone, that may be true for f/4 lenses of common focal lengths which I guess most people like me use. Providing they are not out of spec in the first place.
However, if you have f/2.8 lenses, or very long zooms, or certainly fast primes - all of which are more critical of focus - then you may benefit more from giving them a tweak. I would just say keep the distances real world, and check at different focal lengths.