The crispest I could get was 800x600 dot-by-dot, fullscreen. There's still some wasted space onscreen, but that's the largest I could get the active window without it looking terrible. 640x480 (any type) and any other resolution on full or aspect are terribly fuzzy regardless of filter, and the dot-by-dot resolutions higher than 800x600 simply make everything too tiny.

Well since you're scaling it from 640x480, the next integer steps would be 1280x960, 1920x1400 and 2560x1920. Anything else is going to be blurry because you're scaling by a non integer factor. Also you need to make sure your graphics card is set to centred timings otherwise that'll be applying scaling and making it blurry.

Logical but not helpful since this game blurs every resolution except 640 x 480 no matter the settings. I don't know what you're talking about with centered timings, I've never heard of such a thing, but regardless I have many games which do 2x or 3x scaling just perfectly so the video card isn't to blame.

Just to be certain I took 2 screen captures, one at 640 x 480 and one at 1280 x 960. Went into my graphics program and did a 2x resize on the 640 x 480 and the difference between that image and the captured 1280 x 960 is night and day. The game is clearly blurring at anything but the native res.

Well that's pretty conclusive. I guess they opted to use a bilinear scaling method regardless of the resolution. Usually games will either offer bilinear scaling to any resolution, or nearest neighbour scaling to integer multiples. It's not often I come across things that offer both.