Diaper boxes; rough cut cardboard for flat bottom plus a little Gorilla tape on bottom, not really (reliably) stack-able, but works well. I have plans to build some wood crates that can stack, but that is on a long list of other things i plan to do.
THAT SAID, after making a couple of the boxes from the thread above, I've just reverted to milk crates. They stack easy, are reasonably cheap on Amazon (or were the last time I bought any) and fit longnecks 5x5 or fliptops in a 4x4 configuration.
I store my empties upside down in a round rubbermaid tub (after rinsing thoroughly) in preparation for sanitizing. The full bottles I keep in plastic cases designed for beer.