Thanks for your response.
I initiailly thought it may be the way my card drivers handle DirectDraw, but I've done a lot of research, and this doesn't seem to be the case. I'm running an ATI Radeon 9200 with the Omega third-party drivers.
Also, you mentioned Vista versus XP. Actually, DirectDraw is only emulated in Vista, and this is why you don't see the bilinear effect. If you disable DD acceleration in XP, (in other words, you make DD emulated) then it will have the same effect -- there will no longer be a bilinear filter in place. However, many games / emulators require DD acceleration to run in the first place. Disabling it means I can't use most of my emulation software any more.
As far as I can tell, this is something exclusive to DD itself. I think DD mandatorily imposes this filter, and there is simply no way to deactivate it. That's why I requested that the author of SNESgt add Direct3D or OpenGL rendering support. Using either of these rendering methods always gives me a clearer image without the filtering effect.