I still use the pet bottles that came with my Coopers Home Brew kit a year ago. They've been through 11 batches now, no problems. Like many of you, I rinse the bottles out after use then store them up for sanitising day.
I rack to a secondary fermenter. After cleaning out my primary, I fill it with iodophor solution to sanitise. I steep my bottles and caps in the solution, ready for bottling the nectar in the secondary.
Most nights I will enjoy a glass of homebrew, but found that the 750ml PET bottles are too much. As I don't always drink the same style beer sequentially, I find that the remaining beer loses its carbonation in the fridge over the period of a day or two. My solution: Cascade or Bundaberg Ginger Beer bottles.
The PET caps fit the Ginger Beer bottles perfectly, affording me the best of all worlds: the ease of screw caps, the benefit of glass bottles, and the smaller size of 375ml per beer.
I've been doing this for about 11 months now, and I've never had any problems with carbonation using recycled ginger beer bottles. They're easy to source too, I collect them from my work colleagues. In exchange, they get a few samples of each of my brews.
Happy Brewing