My name reveals my bias but my vote goes to the P-38. When discussing the best fighter of the war it's important to consider an aircraft that was involved in the war from start to finish. I may be mistaken but I believe that limits us to the Bf-109, the Spitfire, the Zero, and the Lightning. The Lightning was by far the most versitale of any of these remaining contenders and so it gets my vote.
I also think that the P-38L has to be considered one of the best period. It had range, speed, climb, killer firepower, and the versatility to fly any mission a fighter might be asked to fly. I've read comments from both German and Japanese pilots that a P-38 would turn a lot better that people would admit and the L with it's boosted controls would outroll a FW-190 at high speeds! I've got tons more I could say, but I'll leave it at that.