Perhaps Jeff Hanneman from Slayer for the best dirty, funky, dark riffs after Black Sabbath. heh
Yeah I forgot all about Hillage - still going strong. Met him at a Manchester Megadog all-nighter about 10 years ago, nice bloke... good tunes.
But Zappa has got to be one of the greatest - taught little Stevie Vai all he knows ;P
Also, if you expand the brief to include bass guitarists (especially if you consider 6-string bass players), squarepusher's pretty good...