I really hope no one says Gordon Freeman or any other interchangable silent protagonist. Freeman does nothing you don't order him to do, unlike Samus who at least has the cutscenes to setup her personality. You could swap him for Rosie from the Jetsons and nothing would change. Even my M&B characters have more character development and personality than him (especially Finkleberg).
Doom Guy is a far better character. Even though he only gets a few text screens to show the kind of person he is, you know he's a demon killing bad ass space marine who is hellbent on killing demons because they killed his pet rabbit Daisy. He has more character development than a lot of spoken characters these days who are generic action hero # 633239 with pre-recorded "witty" one-liners #87723-87726 and quite often voiced by Nolan North (who isn't these days honestly).
But I'd say the best character would be Snake. A tired old wardog who fights because he has to. He doesn't make very many "witty" comments, making the ones he does make stick out more (case in point: MGS3's codec call to Para-Medic about a fish, "Not all I love ancient fish." "Why?....." "They taste pretty good." ) .
