I use the NTSC filter in snes9x-gtk, call me crazy but it seems like it's slightly smoother in software mode. This seems odd to me as usually anytime I need a filter in other emulators, opengl is either mandatory or performs better. Don't get me wrong, it seems to work fine in opengl too, software just seems a tad smoother to me or more likely I have no idea what I'm talking about
EDIT: Oh when I say smooth, I mean performance smooth (scrolling etc.) not pixel smooth.