I don't know. There were so many great aspects in season 3.
First and foremost - I ADORED Naley. I loved the angst at the beginning and the slowly rebuilding their relationship to renewing their vows. Everything about Nathan and Haley were perfect (I use perfect loosely considering there are some small things here or there I would change but in general it was perfect). I loved seeing them fight for one another - proving (to me) why they are the best couple on the show. The one couple who fought tooth and nail to keep together. I loved that.
Peyton became a favorite character of mine in season two and that continued in season three as well. I loved the Peyton/Ellie storyline. It was so bittersweet. And I really loved seeing Peyton as a single teenager, struggling with things other than boys. Yes, she had Jake and Lucas and Pete (major eye roll with that one) but they weren't really a big focus for her throughout the course of the season.
I also adored Skevin. I have such a soft spot for Skills and Bevin, and it was nice to see Skills with more focus in general.
I hated how Brooke treated Rachel (when it was unjustified) and wanted to strangle her but I won't lie - some of it made for some great entertainment. The two girls snarking at one another was kind of fun at times, especially in 320. I loved Brooke defending Mouth. I really loved the Brouth friendship and Rachel did lead Mouth on so I had no problem with Brooke calling Rachel out on that.
I loved the group scenes - the girls together, the guys together, and the whole group like in 318 (one of my favorite episodes of the series).
316 - while I do think this episode was slightly overrated, I still LOVED it. It was so powerful and such a conflicting good/bad message. It really did something for each and every character so as a whole it was good. And Dan killing Keith - was so unexpected. I was never really a fan of either guys (they both annoyed me to no end) but it was heartbreaking to see Keith get shot. And it did make for a great storyline for Dan.
Brucas and Brooke's insecurities/game playing were annoying as hell but luckily, I didn't watch the show for that so I can easily just fast forward through those scenes. But I did enjoy Brooke starting COB - that was a great thing for her character.