In my opinion Little Wing by Stevie Ray Vaughn is the answer. He took an already great song by one of the greatest guitarists ever and found a way to improve it. That's kinda hard to beat.
Re: What is the greatest guitar instrumental ever? 02:33 on Thursday, April 29, 2010
Marty Friedman's Night is my favorite acoustic. As for electric, maybe Satch's Made of Tears or Jason Beker playing Paganini's 5th Caprice.
And Eruption is just epic.