I did some research on this back in 2007, not sure if it still applies.
Stop all those favicon 404s!
At that time, using the rel="shortcut icon" in addition to rel="icon" was to address compatibility issues with IE which used the rel="shortcut icon". I've done some quick scanning and it appears that this was an issue up to IE6. IE7+ appear to support the rel="icon" which is the official link type.
22.214.171.124 Link type "icon"
I still use both but I haven't researched the latest on compatibility issues such as those back in 2007. Anyone else got any updated information on use of both rel="shortcut icon" vs rel="icon"?