My favorite is season 4, closely followed by 3. I loved Leyton getting together; Lucas figuring out what happened to Keith and writing his novel; and the team winning the state championship or whatever that competetition was. Upon rewatch, the basketball scenes and games become somewhat of the highlights of the series for me, whereas I didn't care for them before. I also loved Lucas coming to terms with his heart condition; and Dan going through his crisis of consciece. Oh, and Rachel and Brooke.
Then again, season 3 has all the great Brucas scenes, the two of them are really cute though I prefer Leyton; Lucas and Peyton's platonic friendship; the beginning of Bevin and Skills; Pete Wentz; some great Karen/Deb moments (love their dynamic); the school shooting; and Naley reuniting.
Least favorite probably 5 and 6, I didn't even bother with 7-9. 1 and 2 (gave us Andy!) are both okay-ish, great even, but not as good as 3 and 4.