The last fight between Ryu and Ken happened in 3rd Strike. From their dialog you can realize that Ryu lost to Ken once, but beat him at least twice.
Quoting some of their pre-fight dialog:
Ken: Okay then, I'll make this quick and easy for you. Prepare for defeat!
Ryu: You may think so, but I've still got the better win record. Stand Strong!
It was a friendly fight and Ryu managed to win it, which means he beat Ken at least 3 times and lost only once.
Darkstorm Zero
Actually... I don't recall Ken Equalling Ryu... The only time Ken ever defeated Ryu was in Alpha 2, and that was when Ryu was distracted.
I could cite the fact that Ryu defeated Akuma, while Ken received one backhand from Akuma and was knocked out... And no, Ken was fully attacking Akuma during this One hit KO wonder.
Actually I have one correction to add. Ryu did not defeat Akuma in their SFA fight. They fought, but Ryu didn't beat Akuma. It was Akuma who wasn't satisfied with Ryu's performance and was angry as Ryu didn't let the dark site overtake him, which resulted Akuma punching and destroying the island. There was no winner in that fight.
I've seen the rumor of Ryu beating Akuma in that fight in several forums, but that really didn't happen.