Is there really a difference besides the price? Water cooler bottles are designed to store water for long periods of time so they shouldn't leech off flavors. Is there something else that's special about better bottles?
If you're talking about the water bottles marked with recycling code #1, PET, they are pretty much the same. Of course, you can't get 6 gallon water bottles.
I know some of the water bottles say not to use anything but water in them. I assume those are the ones NOT marked #1 recycling code. Also the water bottle may need a different size rubber stopper.