I've used the 1/8" and 3/16" sizes. Use the larger thickness for bigger windows to add stability. I use car door edging for the molding and either silicone or plumbers goop to hold on the window. No problems yet after 1 year and 3 computers.
I'm going to finish installing mine tonight and i used 1/8 thickness simply because the window molding that I got from 2cooltek had a 1/8 inch groove for the window to sit in.
1/8" will be more than adequate for just a window. I have a "water window" and I use 1/4" for that just to be safe. 1/8" would have worked too, but the 1/4" allows so room for error and it makes working with it easier as I don't have to worry about cracking while drilling, cutting, and milling.
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