Their best one was the Iron Man at Bragging Rights, but that's not saying much. I'd be perfectly fine with neither of them wrestling each other again. Randy Orton never looks better than John Cena in the matches. Infact, he has never ever beaten him clean.
Orton, as a heel, looked quite strong against Cena. Also they have great chemistry, just look at Meltzer rating.
Summerslam 07 Cena Wins ****
Unforgiven Cena wins
Orton then "injures" Cena
NWO 08 Orton retains
Summerslam 09 Orton wins ***
Breaking Point Cena wins ****1/4
Hell in the Cell Orton wins clean
Bragging Rights Cena wins in a close match ***1/2
So Cena wins 4, Orton wins 3. Looks pretty fair to me.