I say Sergeant Johnson since he's been the only individual character to appear in all the Halo games (except Halo wars).
I bet everyone's going to say Master Chief, but everyone is entitled to their own opinion. I personally say Master Chief is more of the Focal Character, the focal character's emotions and ambitions are not meant to be empathized with by the audience to as high an extent as the protagonist (this is the main difference between the two character terms). The focal character is mostly created to simply be the "excitement" of the story, though not necessarily the main character about whom the audience is emotionally concerned. The focal character is, more than anyone else, "the person on whom the spotlight focuses; the center of attention; the man whose reactions dominate the screen." And I personally felt more sad when Johnson died, than when Master Chief had been MIA, I would have still felt worse for Johnson.