Someone's already said Iommi/Butler so I'll go Fast Eddie/Lemmy, neither were virtuosos but they blended perfectly.
One highly underrated combination: the DeLeo brothers, Dean on guitar and Robert on bass, in Stone Temple Pilots.
At the risk of being a bit obscure, I though Steeleye Span's Robert Johnson & Rick Kemp were an amazing duo back in the day.
In 'rock' (the ones that stand out instantly for me): Ramones Cactus Yardbirds/Cream/Led Zeppelin Jefferson Airplane/Hot Tuna Velvet Underground Buffalo Springfield Moby Grape Flamin' Groovies Mott The Hoople Redd Kross Teenage Fanclub Pixies Way too many to name in jazz/funk/R&B.
Shawn Lane and Jonas Hellborg is as sick of a guitar/bass pairing as you find, right up there with Allan Holdsworth and Jeff Berlin.
i didn't read through this entire thread, but i'm going to go ahead and add an additional pair--they may have been added already: Alex Lifeson and Geddy Lee -- they always seemed to have a very strong connection.