The May issue of Guitar One has a list of the 200 greatest guitar recordings of all time. Yet rather than try and compare Robert Johnson to Dimebag, they broke it down into 10 genres. I'll give you their #1's for each:
Classic Rock: Appetite for Destruction, GNR
Blues: Live at the Regal, B.B. King
Metal: Paranoid, Black Sabbath
Jazz: The Incredible Jazz Guitar of Wes Montgomery
Country: Guitar Legend:The RCA Years, Chet Atkins
Shred: Rising Force, Yngwie Malmsteen
Modern Rock: Rage Against the Machine, self-titled
Soul/Funk/R&B: Green Onions, Booker T. & the MG's
Acoustic: 6 & 12 String guitar, Leo Kottke
Instrumental: Walk-Dont Run:The Best of the Ventures

Of course I've never heard 1/2 this stuff, but I was going to recommend that Leo Kottke one anyways, that's what made me think of the mag. Let me know if you want me to expand in any particular catagory. I'm not the one saying these are the best of their respective catagories, so don't anyone come back saying..."What are you thinking? ____ by ____ is way better than ____." Yet the comlete list was pretty comprehensive, almost everyone I listen to is in it somewhere.