GLQuake

resamples all of them using a crappy "nearest pixel" filter. The result is that you see specific rows or columns of pixels being repeated. Spirit's screenshot shows this, you can see what looks like columns of double-wide pixels but actually that's just two columns with the same exact pixel colors.

Fitzquake

1. hud/menu graphics, model skins, and sprite frames: images are padded with empty pixels to make them powers of two, and texture coordinates are modified so you only see the actual artwork part of the image. This means they look as good as power-of-two textures, since there is no resampling or distortion.

2. world textures: since they have to be able to tile, these textures can't be padded, so they are resampled using bilinear sampling to be a power-of-two size. This still degrades the image somewhat, but looks better than glquake's resampling.

Aguirre's glquake

Aguirre does bilinear resampling, similar to fitzquake, but for all images. So menu/hud/skins/sprites are also somewhat degraded, but not as bad as glquake.

Other engines

not sure, i haven't researched other engines.