They never make it clear who Nathan's bestfriend is. In season 1 and 2 they always said it was Tim, but Tim just seemed like Nathan's sidekick. Also, in one promo for the show the voice over said that Skills and Nathan were bestfriends, but I never really saw them as so close. So that leaves Clay and Lucas. Oops sorry I should have mentioned not to pick Haley... like his closest guy friend.

I think that where he is in his life right now, it's Clay.
Lucas was always his best friend and brother. He loves Lucas but now that he is gone, Clay and him are really close. Not that Clay replaced Lucas, but at this time they are closer then he and Lucas are.

No one can replace Luke, thats his big brother. And he misses him. Its a different relationship with Clay then it was with Lucas.

Lucas. He may have left Tree Hill but that talk with Jamie made clear that Lucas will always be his best friend.
Clay is also one of his best friends these days.
Skills was more of a best friend to Lucas, he never was that close with Nathan.
Tim was like his sidekick to his bad schemes.

I t used to be Lucas,now it`s Clay.

^ Agreed, Eliza.

Right now? Clay, definitely. Who else is there? ( =