The long instrumental intro to Sails of Charon by the early Scorpions is a great part. This is where I first heard classical guitar riffs employed on an electric guitar. I think Uli Roth is an overlooked guitarist who should be up there with the Eddies, Steves, and Joes of rock guitar.
Also, of course, Surfing with the Alien, by the great Joe Satriani which got a lot of people seriously into instrumental guitar music. There's so much in that one song that was completely new to guitar players that it's the song people most refer to when trying to find the birth of crazy shred guitar. His first solo going in starts with a two hand tap with pick which is impossibly fast followed by regular very fast playing probably never before seen, then some crazy harmonics working with the dive bombing trem. The transitions of all these styles, all thrown together back to back to back are so seamless few can achieve Joe's fluidity. This was when I first realized that a guitarist could take the hard rock guitar solo genre beyond Eddie Van Halen.
And since we are talking about people named Joe, Joe Pass and his solo work (especially Virtuoso) is just amazing. He sounds like two or three guitarists all at once. His fingerstyle on this body of work is timeless.
Keith Jarrett goes to another dimension and back when he plays piano. It's so hard to describe I won't even try. His bizarre buzzing sound me makes while he plays kind of fits his music though some people don't like it.
Best instrumental music for me is just about anything Coltrane. He takes the instrument which is probably closest to the human voice (as opposed to piano, guitar, bass, or electronica) and uses his breath to emote on the saxophone. I don't know if it's pain or happiness, but his music will always live on.