Preview has surprising abilities ...
Import your icons into Photoshop - The Unofficial Apple Weblog (TUAW)
Basically, the trick is to open the application's icon in Preview (as was pointed out in the comments, you can most easily do this just by copying it in the Finder and selecting "New from Clipboard" in Preview's file menu), then save it in Photoshop (PSD) format. Now you can open it in Photoshop and get access to the image for editing, including the alpha channel.
I've usually done a get info to see icon, clicked on it, then cmd-c then open in preview.
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