Beatboxer did a great two part post covering this subject in detail. The conclusion was that Hopkins had the slightly better resume and that was before the Pavlik win.
Hopkins was defending a unified title for several years whereas Joe only held the WBO and only unified when there were fighters prepared to come to him with their belts. That's one of my issues with Joe and why I don't consider him the better fighter. I felt Hopkins won the fight with Joe and I think Joe should have given him a rematch rather than retiring after his showboating cringefest with Jones.
Did he? I have watched it three times and only had Calzaghe winning live, when I was seriously leathered.
Losing to Hopkins isn't anything to be ashamed of, lots of people tend to bash a guy for losing a fight, or performing poorly. Had Calzaghe lost to someone like Ashira or Sheika I would have piled in. Calzaghe is a great enigma IMO. The guy was past his best before anybody outside of the UK knew who he was. After beating Eubank, which was a very good win at the time, he was doing nothing for the best part of nine years, defending a single belt. There was no building toward anything, no unification fights, nothing. He then runs into the highly touted Lacy, and beat him so badly that his opponents name has how become a metaphor for a one sided ass-whipping. He had a very good career, but it could have been so much more. 46-0 with that resume isn't as good as, say, 43-3 with better opposition on it.