I don't remember if glass windows have quality modifiers, but i imagine they do. So you're looking at 3x clear glass gem base value (x whatever the gem window modifier is, if there is one) vs. glass window base value x quality modifier. I'd have to go look up specific values and do some testing to get an actual answer on this one...
Done.
Clear glass gems are worth 25 dwarfbucks each. So, minimum value for a clear glass gem window is 75 dwarfbucks.
I don't have the economy, so guesses as to value are within a range:
I designate a nine-sand-square office with a no quality felsite throne (10 dwarfbucks). The room registers as meager (1-99 dwarfbucks); experience says it should be 19 dwarfbucks (10 for the table, 9 for the 9 squares). I throw in a clear glass gem window. The room continues to register as meager. This gives us a maximum value for a clear glass gem window of 80 dwarfbucks; likely value is indeed 75, indicating gem windows give no value multiplier.
The gem window is then disassembled, and I put in a new gem window made from gems worth 210 dwarfbucks (150 + 50 + 10). If I'm right about no modifiers on the value of gem windows, this room should be worth 229 dwarfbucks. A check shows that it is now classed as "Modest" (100-249), so the theory seems to be confirmed.
A no quality clear glass window (non-gem) is worth 125 dwarfbucks; with clear glass having a value multiplier of 5, this indicates that windows are of an equal value to statues. A masterpiece clear glass window is worth 1,500 dwarfbucks.
Moral of the story: glass gem windows are a waste, even for a dabbling glassmaker. You are much better off, value and resource wise, making a window from the glass furnace directly. Gem windows seem to be useful if you really, really, really, really, really want to have a colored window (or perhaps to make a disco wall). Gems are otherwise better used for encrusting, as encrusting something with a cut clear glass gem adds at least 50 to its value, even with a dabbling gem cutter and dabbling gem setter.