GSP Serra II
Of the two you listed I'll say Jones/Shogun by a fair margin, but all time it has to be Silva/Franklin I. That was a beating for the ages.
JDS vs Cain. Everyone keeps mentioning how fast or volatile the end of the fights were for Rua or Franklin, but I think it is because of the lack of an ending that Juniors loss was so harsh. Because he didn't lose a fight to one strike or several, he lost it to his own gas tank. Hell, he couldn't even raise his hands to defend against some of Cains strikes in the 2nd through 4th!
Ah yes i remember this fight it was a one sided brutal anal r@pe.
Jones - Rua
not even close
Franklin got nasty broken nose, but it only lasted 1 round