Love your links!
Jan Akkerman (left channel, Focus) & Peter Banks (right channel, original Yes guitarist and Flash) - "Get Out Of My Fridge"...
http://www.youtube.com/watch?v=IsZaFAiXxHU
Steve Morse (Dixie Dregs) & Steve Howe (Yes) - "Up In The Air"...
http://www.youtube.com/watch?v=ZhbZ9NNBM28
Here's Steve Morse and Rik Emmett (of Triumph) playing the same song in the studio;
http://www.youtube.com/watch?v=_3XdLlLBvm4
Kim Mitchell (of Max Webster) & Alex Lifeson (of Rush) played together on the Max Webster song "Battlescar"...
http://www.youtube.com/watch?v=PD2aep1ge7Y
Stevie Ray Vaughn & Albert King...
http://www.youtube.com/watch?v=gZB57b3lPQE
Chet Atkins & Les Paul...
http://www.youtube.com/watch?v=HfjD680wQJI&feature=related
Les Paul & Jeff Beck...
http://www.youtube.com/watch?v=LrC_oqWq2pU
The "Les Paul & Friends" concert DVD and album was great too...everybody from Steve Vai, Neal Schon, Eric Clapton, Keith Richards, Eddie Van Halen, Billy Gibbons, Buddy Guy, etc was there...great show! Unable to find a link to the jam though ;(
Johnny Winter & Leslie West - "Red House"...
http://www.youtube.com/watch?v=Kh4zc288ERg
This G-3 set was pretty cool too...Stevie Vai, Eric Johnson, & Joe Satriani - "Redhouse";
http://www.youtube.com/watch?v=ZxZXHStulr4
The entire "Friday Night in San Francisco" album with Al Di Meola, John McLaughlin and Paco de LucĂa is fantastic...
http://www.youtube.com/watch?v=nlaCZ106b5w
I have many more favourite collaborations besides these...but there's a few anyways :)