Hendrix Experience, Hendrix and Noel Redding, just perfect together. "manic Depression" is a perfect example, especially the central guitar solo section.
Impossible to name the "best" as it can come down to a matter of taste, so many great ones. But a particular favorite for me is Grant Green and Ben Tucker, example "Green Street".
I haven't read through the thread so apologies if my pick has already been brought up, but Geddy and Alex have my vote.
So many great combos already mentioned so I will go more obscure: - Rory Gallagher & Gerry McEvoy - David Clark Allen & John Glascock (Carmen) - Jon Camp & Michael Dunford (Renaissance - where the bass was often the lead and guitar the color)
Several deserved mentions of Clark-Di Meola, but I think the Di Meola/Anthony Jackson and Di Meola/Tim Landers pairings of Al's early rock-jazz solo years were ridiculously great as well.
Just revisiting this thread at the same time Scar Tissue by RHCP came on the radio. The interplay between John Frusciante and Flea is incredible - so complimentary and fluid.
When you hear the following song, it is very hard to argue with your assertion: "Barbarism Begins at Home"