The method I use, and it works very well for me, is to do the following:
1) Turn PSI on CO2 down to 2-3 PSI.
2) Vent all kegs.
3) Run about a pint from each keg.
4) Fill bottles directly from the tap and cap on the foam to reduce oxidation.
You're going to make a bit of a mess. So long as you have a few towels down, you can minimize the mess. It also helps to have a second person to help; my wife fills the bottles, I cap, and wipe them down. I make sure that I sanitize my bottles with Starsan ahead of time. I'm sure the beer gun is nice and all, but I'm a cheap bastard! I did try a porter I bottled before Christmas using this method last night, and it was carbonated perfectly. I could not taste any oxidation or off-flavors.