black bars are quite common in screenshots (e.g. on RHDN), and definitely better than smudging. and there's more than cropping going on, since those resolutions seem to have a multiplier of 2 or 3 applied (either by emulator or by GIMP).
as mentioned, emulators should have a button to do a raw, non-enlarged output. also, Alt+PrtScr should just capture the current window, saving you a little work.
if black bars are somehow a deal breaker for you, that's fine. but if your motivation is tidy-looking images, then realize how the non-integer resizing appears to some website viewers. there's also filesize/bandwidth issues in having an image with 4x or 9x the needed pixels (as you're just scaling them back down anyway), but that's outside the purview of my whining, as i don't have dial-up. ;)
