I think it's just because Nintendo keeps hammering us with these franchises that they are just the ones we know the best and therefore are awesome.
Who's the ultimate female badass? Samus, this thread shows that (what, a 30 point lead over everybody else).
Who's the ultimate gaming hero? Link.
Who do we think of when we think video games? Mario.
I don't think it's so much because we're all Nintendo dorks, it's just those characters have become icons for gaming.