Depending on how low res low res is. If it's like, GameBoy, I usually play at 2 or 4x depending on the emulator, and usually 1:1 on PSP. If it's a DVD quality show/movie/whathaveyou I'll usually full screen it.
Windowed but bigger than original resolution with the filters to make it look better for gba. I used to prefer full screen but now since i chat windowed works better for me. Either way if u have a huge screen windowed on that big screen will still look big XD