cleaning beer lines comes up fairly regularly around here, so i figured it might be good to have a place where we can talk about what we do.
i have a four keg system and while i have many more kegs than that, i don't currently plan on expanding my number of faucets. my general technique is to simply flush all the lines out anytime i clean a keg.
i clean out the keg and put 2 gallons or so of warm star san into it. then i pressurize the keg and shake it all around to get the sanitizer into all knooks and cranny's.
after that, i leave the keg on a gas line set around 3-5 psi and hook it up to the first faucet.
i allow the star san to flow out of that faucet for 20 seconds or so and then i disconnect the faucet and using a tiny brush, clean out the faucet head.
then i hook it back up, flush for 30 seconds and move on to the next line.
an important note is that i leave the star san in the line. because it is acidic, it has lots of time to break down any beer stone that may have accumulated.
the trick here is to remember that the lines are full of star san, not beer, so pour that first bit out when you pull a pint off each line. truthfully, if you forget this, no harm will come to you (ask my wife) the beer just won't taste right.
i have never noticed any damage or discoloration to my lines by leaving the star san inside them, sometimes for as long as a week on a keg of beer that i didn't particularly care for.
using this system , my lines get cleaned out every 3 weeks minimum. they are all two years old and i have never changed them as no discoloration or funkyness has occurred.
the only bit of funkyness i have encountered was traced back (eventually) to irish moss being stuck inside a dip tube on a keg and releasing from time to time. this was easily fixed by removing the dip tube and blowing it out with an air gun after a soak in star san. it was prevented in the future by switching to whirl-floc tablets.