I've got a 16:9 display with a native resolution of 1920x1080. In the world of Cortex Command that equals to 960x540 due to 2x mode which doubles all pixels. Which resolutions should us 1920x1080 users choose? Windowed or full screen (preferable full screen). I've noticed when I turned the resolution down to 1152x864 everything looks crisper and cleaner, at the downside of stretching the image.

1920x1080/960x540x2 looks just fine to me! Maybe I like the crisp 2x scale.

I just like 1080 at full screen. I've played this game for so long now with awkward resolutions it's not even funny. Might switch around some day, though...

for windowed mode just 2x the smallest window size if you have low system specs, or 2x 1600x900 if you have a higher end PC and want to see around the window a bit, (say you're using IRC or what have you) and just one step down from 1920x1080 2x windowed if you want biggest possible outside of fullscreen.

interesting thing about just 2xing the VGA mode is it make the game window a rather nice ratio of W:H while still occupying a significant chunk of my screen. (I have basically the same thing as you with my monitor)

I like 2x'ed 960x520 windowed, for my 1920x1080 monitor.

It fills the screen, except the taskbar, so changing windows midgame is no issue. The resolution itself isn't too far from the 640x480 that CC seems to be made for, so it doesn't seem like cheating or anything, and it's crisply enlarged so it's easy to see and read everything.