Top 5 guitar jams

MIck Tayor on "hear me knockin" from Sticky fingers
Hendrix "hear my train a comin"
Zep "stairway"
ac/dc "the jack" "let there be rock"
Little feat "waiting for C."

Glass Harp (P. Keaggy) - Never Is A Long Time.
Lou Reed / Steve Hunter - Intro/Sweet Jane
Just too many to isolate just 5 but Allman Bros., Jeff Beck, Stevie Ray V., and Chris Whitley would make my list with a whole lot of their art.

Eddie Hazel (Funkadelic) on Maggot Brain. For me, the greatest of all rock guitar solos.

Clapton - Go back home/stephen stills
Mick Taylor - time waits for no one
SRV - Walking the tightrope
Jimmy Page - In my time of Dying
Neil Young - Love to Burn

Here's some that come to mind:

Without the album in front of me I can't remember the specific song - been a long time - but the live album, "Four Way Street" by CSN&Y has some real goodies.

"Child In Time" by Deep Purple

"No One To Depend On" by Santana

From Buddy Guy's Live release, "The Real Deal" there are some absurdly good jams between Buddy and G. E. Smith, particularly, "Damn Right I Got The Blues" (check out the DVD).

There are various versions, but the best live versions of "Red House" and "Here My Train Coming" by Hendrix are available on some of the unofficial releases after his death. The full version of "Here My Train..." from live at Berkeley is ridiculous.