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The GIMP, Photoshop, Paint Shop Pro, MSPaint, or whatever graphics program comes up with "save as"; which file type should you use?
PNG, JPG and GIF file formats are standard on the web (where most webcomics end up). The fancy PSD and XCF formats are specific to certain programs, a very poor choice. And TIFF and PCX, they've gone the way of 5" floppies. The other formats have uses. While working on a comic, saving in the editor's native format has benefits. For one, you can place parts of the image on layers, making it easier to edit or colorize.
GIF is best used when you have very few colors. It's best to be careful using them though; some programs will try to force GIF images into the web-safe color palette by default. For pure black & white of course, there's no problem. GIFs do have a strange behavior when corrupted: while most images will not display, a GIF often leaves strange Venetian Blind patterns.
JPG is a bad idea. The compression (unless done by a good program) can reduce image quality. It can't handle palettes, so an image with few colors will waste memory. Although usually not needed in comics, JPG doesn't support transparency--this may require you to carefully crop the image or match the background exactly.
PNG rectifies most of the problems: it can use palette or true color depending on the circumstance, includes decent compression without loss of quality and contains many advanced features.
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