i voted for the portal one for the companion cube... and then the old school 8/16 bit ones.
in general, i don't like the silent protagonist because too often they are silent when people talk to them. portal kinda works because the main character is alone and has no one to talk to (although at some point she might get tired of glados taunting her and yell something back).
i dont get the lovefest for Gordon Freeman/Link as silent heroes. Fans say, "Oh, i am Gordon Freeman, the everyman! if he talks, it's no longer me." and if you were mute, you'd have a damn good point. what breaks the immersion for me, is an NPC talking to my character, asking a question and my character doesnt respond. "Gordon Freeman! How have you been? it's been a while, are you doing okay?" oh, it's awesome that Gordon doesn't respond! that's exactly what i would do in the same situation! i would be a dick and never talk to anyone!
same complaints apply to link.