I think I have advice with the JPEG, actually. You see, my comic was originally exclusive to my computer since I didn't ever think it would be good enough for a website, and they were all saved as JPEGS since I hadn't been told otherwise. When I finally decided to use SmackJeeves, I traced over the JPEG speckles in Paint and saved them as PNGs. However, my comic is mostly screenshots and non-sprited drawings (a few sprited scenes here and there), so your equivalent would be putting non-JPEG sprites over the JPEG sprites and saving it as PNG, then tracing over as many of the remaining JPEG speckles as you can.
I just saved it as JPEG by accident, I don't usually do that, I've got the original BMP still saved, so I can just go back and save again as a GIF or PNG, I'll probably go with PNG from now on.