I get a lot of my bottles from friends who donate their empties to me, and they may or may not have been rinsed. They've also been sitting in their garage or basement, so who knows what's taken root in there.
So, my procedure, which is a pain in the butt, but gives me piece of mind is:
Soak all my bottles in tubs filled with hot water and Oxyclean for 2 days. This gets any labels off, and also loosens up any gunk inside. I usually soak a few extra bottles, since not all of them get through the procedure.
After that, in the sink, I use a bottle brush on each bottle to make sure it's clean, rinse, and give it a quick peek through the bottom to make sure there's nothing stuck. If there is, I toss the bottle. There's usually about 3 I can't save.
As I'm done with each bottle, it goes into the dishwasher. Bottom rack. My dishwasher can't do just a short cycle in combination with the extra hot wash, so I do a full cycle, extra hot with no detergent, and the dry cycle for the heat.
When they're cool, I bottle. I pull the bottles from the washer, give each one a few bursts of Star-San from the Vinator, bottle, and cap with caps that have been sitting in the Star-San in the Vinator's reservoir.
Like I said, it's really time consuming, but it's also really thorough. Since I give away the majority of my beer to friends, I want to make sure I don't give them moldy bottles. If it was just for myself, I might not be so paranoid.
-A