What is the best method to sanitize the beer lines for kegs? iodophor or star-San?
either or - whatever you have on hand.
Are you looking for cleaning or sanitizing? Title suggest one and post suggests another.
I clean with Oxiclean that I run through with beer line cleaner pump that is featured on the AHA. http://www.homebrewersassociation.org/pages/community/pimp-my-system/show?title=pimp-my-system-beer-line-cleaner
I sanitize with Star San ( gave up on iodophor years ago due to discoloration and smell ).
I use BLC (Kegco Deluxe Hand Pump Pressurized Keg Beer Dispenser Cleaning Kit with 32 oz. Kegco Cleaner | BeverageFactory.com) in a hand-pump pressurized bottle.
Note that most (all?) of these will have a connection to attach to a Sankey, not a Ball-lock. I cut the Sankey connector off and put an adapter on, to which I screwed a ball-lock post. So now I just attach the black ball-lock connector to the post on the end of the hose and pump cleaner through it, and out of the faucet.
I use PBW for cleaning the lines and the kegs. I use StarSan for sanitizing. I move the PBW through the lines using a bicycle pump connected to the barbed connector of a standard quick-connect.
The best thing to clean the lines with is Beer Line Cleaner, and if buildup has become an issue, use an Acid Line Cleaner first. Now being that StarSan is an acid, and PBW is kind of a caustic, you may get some results, but probably not the best results as you would using the proper chemicals in the right order. Using the right chemical for the job will always give the best results.
There is also a new chemical called Desana Max that I will be testing as soon as my lines need cleaning and it is a one-shot color-indicating chemical that is supposed to be the best yet, we’ll see how that goes in real-world use.
As for getting the chemical into the lines, the best thing truly is whatever you have laying around that can be connected 
If you put 1/4" flare connections on the ends of your lines, you can connect anything. I use a corny keg and pressurize with C02 or if I’m feeling cheap just clean compressed air. Garden sprayers are cheap and work great and the hose can have flare fittings attached as well.
I used 4% caustic soda this weekend. worked like a charm but I do want to try some BLC since it should be safer than caustic.
Kai
I’ve gotten to the point where I just replace my beer lines every 4 months or so. Part of it is lazy, but it is just faster for me. I dissassemable faucets and couplers/taps/QDC and soak them in hot oxyclean and hit them with a brush and put it all back together with new lines. New lines don’t need sanitizing, by the way.
I also use BLC. I have a hand pump to run it through the lines. It works great and cleans the lines like new.
Beer Line Cleaner
Any problems with flavor/aroma from the vinyl? I’d be nervous about running beer through without at least a quick rinse.
If the lines are food grade, no aroma/flavor contribution is part of the approval process.
Yeah, but we see occasional bad batches of vinyl line, people complain about it here on the forum and I know a guy who got some from morebeer (they replaced it).
Since mine is all trunk line I use BLC.
Oh yeah, I remember some of those.
I’m not actually worried about the lines themselves, rather any fragments or residues left over from manufacturing.
Or contaminants that get in post-manufacturing I suppose. Unless it came in a sealed bag there could be dust, liquids, etc.
I do rinse the lines out by hand with hot water before assembly. BUt don’t sanitize.
Contamination is not a huge deal post fermentation once the beer is packaged - not saying it is unheard of but it’s not as easy as we make out soemtimes. And, while we are justified in being concerned about contamination, there is no need to be overly paranoid. Not all microbes are beer spoilers, in fact the vast majority are not. Even so, beer line is sanitary enough for packaged beer. There is absolutely nothing to worry about.
A colleague just turned me on to this (http://www.desana-usa.com/desanamax.html). Did you try it? It’s a persulfate cleaner. Looks good (but on the expensive side).
I have used this. A few samples came with some kegging equipment I bought close to two years ago. It works well, but a simple caustic (NaOH) works as well and is much cheaper.