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I've only used an older version, which did transparencies very simply, but the new one has a lot of additional features.
The not-really-new-but-still-hasn't-quite-caught-on PNG file format also allows transparency, so you could find a PNG utility and use that also. The basic PNG file type with GIF-type transparency is pretty univaersally supported in browsers now. (PNG format also supports some much more advanced transparency and other effects, but most browsers don't support the additional functionality yet.)