There are a couple of different storage systems out there that allow you to roll your windows up and store them in a duffel that either attaches to the roll bar or fits in the rear storage area under your soft top. The Clover Patch Roll is pretty popular: 10-ST-9100 - Clover Patch Window Roll™ for 87-06 Jeep® Wrangler YJ, TJ & Unlimited - Quadratec
. Bestop makes one as well: Bestop 42810-09 - Bestop HOSS™ Window Storage Duffle in Charcoal For Bestop and Factory Zip Out Vinyl Windows - Quadratec
. If you don't want to spend that much, you could do what I did (full disclosure...got my ideas off this forum) and buy some felt, cut it into 4 sheets large enough to fit between each window (I have full doors so didn't have to account for half-door windows). Once you layer the felt in between your windows, roll it all up and secure it with a couple of velcro straps. Some folks have actually sewn the sheets together to make little pockets for the window to fit into. If you get a pool noodle and cut it down, then roll your felt-wrapped windows around the noodle, that will keep the roll tight and minimize creases in the windows. If you want some extra protection from moisture and dust, you can then take the bag from a camp chair and slip the roll inside the bag. I think I spent maybe $15 total for the felt, velcro strips and pool noodle.