I use regular ol' plastic shopping bags for clothes and shoes and the like, in my soft Cortech bags.
But they're top-loaders.
You can go all bling-high-roller and use ziplock bags, I did that on my summer tour last year.
Problem is, these bags swing open from a bottom hinge. If things aren't well contained, everything falls out or falls into the open half. The X-straps help a fair amount for larger things like full grocery bags, but smaller items roll out the sides or under them.
I thought about just using some small boxes, but they'd need to be collapsible when not in use so they don't take up room. I usually put my helmet and gloves in one case so I don't have to carry them around or worry about them getting stolen if left on the bike.
I'll check out Aerostitch to see what they have.
