I also use the foodsaver, and have many of my PSK, BOB, and FAK components vac packed. You can cut the bags up and make them very small. For instance, my medications, my fire kit (PJ/cotton balls), and other items that could benefit from being tightly packed and waterproof. I have a very small pocket fak (minor cuts/scrapes, really) no bigger than a credit card (well, about 3/8"thick)which is also so packed.
In my BOB and larger kits, I vac pack clothing, also. You'd be amazed how much you can squeeze down a watch cap, gloves, socks, etc. The advantages over zip lock are that the bags are much sturdier, you can boil food in them, and the foodsaver draws them up much tighter than you can do sitting on a zip lock bag.

I see the primary disadvantage as lack or resealability, and that you have to cut them open (unless you have scary-sharp teeth you're willing to risk). I make mine a good deal longer at the "neck" than necessary. Once shrunk and sealed, I just roll the excess around the bag. That way I have enough material to roll up as a temporary closure once opened.