For me it would be the Boeing 727. In my lifetime I've flown on it 268 times. The DC-9 comes in second. I've been on 130 DC-9 flights. The particular aircraft I've been on the most is Boeing 727-225 msn 20415. I've been on it ten times. The first two times it was Eastern's N8841E. The last eight times it was USAir Shuttle and US Airways Shuttle N922TS.
In case you're wondering how I know, I've kept accurate records of all my flights since I started flying in 1966 (except for one 1947 flight when I was a baby).
Fly Eastern's Golden Falcon DC-7B