Wow I see much love for Gordon here. I for one bought HL1 for CS, but HL2 for HL and CS. I can see how he is popular. However I hardly see how he can compare to Mario... As someone said, Mario is hero 101, he saves the princess, can't do more heroic than this... unless you take link, saving the princess too, but with a sword and shield (and later a horse to make it more epic).
I can't really see Gordon comparing to these two as a hero... saves the galaxy? sure, but so do the others, Link travels between parallel worlds and time, mario goes into space (and in his RPGs he goes in time and in parallel worlds too). That's only a generational evolution, Gordon would never have even been thought of when Mario and Link started off.
Against snake? yeah they are in the same field, i'd say snake is more charismatic, but gordon's feats are more remarkable.
I really think people mistake "greatest hero" with "most cool hero", cause in that case you should always choose James Bond!
Popularity wise however, there is only one real contest.... who can sell anything to the most people? well only one of these can sell multiple sports franchises, board games..... Mario.
Heck I read once that he was more recognizable than mickey mouse... beat that!
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