I was gifted some 4' x 6'6" double pane storefront windows a few years ago - I'm working on the greenhouse now! The trick with using old windows is getting ones WITHOUT a low-e coating. Most new windows have coatings that reduce the amount of solar heat gain and visible light that is transmitted. Sometimes you can see a coating - the glass will look slightly brown, gray or blue. Sometimes you can't see it, but can test for it using a lighter. See here:
http://ths.gardenweb.com/discussions/2595103/identifying-low-e-windows
I bet the glass from old sliding glass doors would make a great greenhouse!
With glass, you'll need a more robust structure than plastic - and you won't be able to move it as easily, but you won't have plastic that degrades every few years either. Also, for those of us in cold northern climes, double pane clear glass is excellent for both light transmission and insulating value.