Here's a demo map:
http://www.quaketastic.com/upload/files/single_player/maps/glass.zip
The trick relies on a "detail" brush which is "skip" textured (which wasn't possible before tyrann's compiler). Skip prevents the brush from being rendered, and detail keeps it out of visibility calculations.
We start with a frame for our glass built out of regular brushes. A na�ve attempt would build a single rectangular detail brush to fill the frame and give it the skip texture. The problem is that the insides of the frame will still get clipped away by the detail-skip brush, so there's a visible gap in the level.
The fix is to build our detail-skip brush in such a shape that it doesn't clip anything away. In the example map each side of the window pane comes from a different brush. Each brush is a square-based pyramid, with the square face exactly filling the frame of the window, and with the apex of the pyramid sitting in the space inside the window (we don't care too much what happens in there because it's out of bounds).
You could pretty much do this already with just a func_wall covered in skip textures, the innovation is that you don't use an entity any more. In theory this also makes the trick mod-neutral, although in practice mods which don't support func_wall are vanishingly rare.