I understand Photoshop pdf preserves the information and can even preserve the mix between pixel and vector information. Most 'photoshop type' applications will accept .psd files probably. The transparancy of a gif file is rather harsh, there is no blend. Alpha channel transparancy can be gradual, so much better. The way to go, in low resolution (72 dpi or 96 dpi for on-screen use), is of course .png. Most current versions of web browser accept it too. If your ps-type app reads it.