Call me an idiot, but I still prefer 3x w/scanlines in the software renderer to GL for most games. Vectors are an obvious exception (even if they were still able to display properly in software), as well as really stretched games like Blasteroids.
Unfortunately, as Jean-Phillipe mentioned, many games display too small even at 3x. Don't suppose 4x w/scanlines is ever coming our way?
I just like the "hard-edged" look you get with the software renderer; the overlays help in GL, but... I guess it's a matter of taste.
Richard: I hear what you call "windowboxing" called "pillarboxing," that is like what a 4x3 image looks like on a widescreen monitor stretched to full height with black bars on the sides. Is there a definitive term, or are we still figuring that out?