I am not entirely sure I can do a complete list of 10 for each, but I'll see what I can do.
 Naley Courting (Season 1)- Definitely my favorite storyline. I have always loved the storyline of a bad guy (or girl) changing him (or her) self out of love for someone else. I also loved how authentic the whole thing was. Nathan didn't do some superhuman change overnight, instead he moved forward and back as he became a better man. Haley also changed, and not always for the better. But ultimately, this storyline brought us the best couple, Naley.
 The School Shooting- While not my favorite story, it was definitely among the best. It was a story that was handled with a great deal of care and respect for all parties involved. They didn't demonize Jimmy or the students who bullied him. Instead, they showed what could happen when people forget about the power of words and actions.
 Luke's Investigation of Keith's death- This storyline laid the groundwork for the redemption of Dan Scott which I also liked (see 4 below). Luke was doggedly determined to find out what exactly happened and to Keith even if it estranged him from his mom. That took real guts and showed the depth of Luke's love for Keith.
 Redemption of Dan Scott- Obviously Dan can never been completely redeemed in the eyes of the people he has affected, but that didn't stop him from trying. What I really liked about this storyline was that Dan didn't just become a weak-willed character, but kept the menace and danger that he had always had, just focused more constructively than previously.
 Deb and Dan's divorce- Especially the couple of episodes where they were pranking each other. While most of the pranks were just downright petty, others were not so much, but they were all quite funny. This story also brought us ultimately to the wacky Deb who was just great.
 Skillz and Deb's romance- This was just hilarious. Skillz is such a cougar chaser. I also loved the whole internet aspect of it (webcam anyone? <snerk>) They were actually really good for each other, particularly after Q was killed. I was sad to see the two of them breakup.
 Peyton and the Record Label- Mainly because it introduced Kate whose music I love, love, love! It also gave Peyton's music obsession a useful adult outlet and showed us alot of really cool bands.
 Lucas' Investigation of Dan (Season 2)- This just showed that Lucas could play the same game as Dan, albeit not quite on the same level, although to be honest, who could? I think it also gave Dan an idea of how determined Lucas can be to uncover the truth when he wants it.
 Nathan's Point Shaving- While I can't say I liked this storyline, it did show that Nathan is still a good guy no matter what he may do. He started off the whole thing trying to provide for his family and then it got out of hand very, very quickly. It also had impact in the 5th and 6th seasons.
 Haley going on tour- Again, not a favorite, but definitely an important plotline. It introduced us to Chris, gave us rockstar Haley which would continue on even into the current season, and ultimately showed Naley's strength.
 Nanny Carrie kidnapping Dan- Hands down the worst storyline from One Tree Hill. It never fit in and was just too weird to really be likable.
 Love Triangles- Take your pick. I don't like love triangles because I see them as a crutch to real writing. If you don't know what else to do, give us a love triangle. They have also been overused and stretched out for far too long. In addition, while they might have been ok in high school, in the post-college OTH, they were just annoying.
 Renee accuses Nathan of adultery- This one just seemed like drama for the sake of drama. Never fond of that.
 Katie stalks Clay- Again, just a weird story which was basically a retread of FauxDerek.
 Nanny Carrie (Season 5)/Gigi (Season 6)- Basically these were two of the more annoying love triangles and again, just drama for the sake of drama.
Can't really think of anymore because #2 covers so many. Tomorrow, I'll try to do Favorite Musical Artists and Favorite Songs.