I had to join in an attempt to put an end to the flame-wars.
Or, to stop the "Silent Protagonists are lame, they have no personality"
Right, I'll keep this as brief as I can.
The silent protagonists do have a personality. In fact it is the very fact that they are silent that endears people so strongly to their personalities.
Put it this way, it is through their actions and through the interactions of those around the character that forge the personality and drive the character on.
A silent protagonist lays away the things that cause hatred towards the vocal protagonist, it's pretty hard to be "obnoxiousness" or "egotistical" without words, well, at least in a video game (grabbing your crotch, that's pretty damn egotistical, but difficult to enact in 1st person view!) (edit: Mirrors Edge could manage it!)
That's not to say they are not flawed, often you'll be thinking "Christ man, just say no!" but that's the same with all games, with Silent Protagonists at least you can have your own mind wander to "I'm only doing this because your momma told me to be nice to you, while I was in bed with her, last night, ZING!". I find it much worse when the protagonist talks and cheers on with a "Sure thing Mister" when given a tedious task.
Further more, the fact that the OP asked "who is the greatest silent protagonist" kind of asks you to ignore the crappy ones who do such mundane things as "go kill 50 monsters for me, then come back here so I can send you again!" so you're left with (or should be) the well-rounded, well written characters.
Now, to say the likes of "Link" and "Freeman" have no personality is absurd. It's pretty obvious what they're like from the interactions of those around them. Nobody comes up to Freeman and goes "Oh, Jesus god, you're not eating another baby are you!" Thus, he is no baby eater! Sure, I've exaggerated but it makes sense!
However people do say things like "Thank God you're here, please, help us" and through the game your character will succeed in doing so, thus, he's a good guy. Even if you're shooting the guy in the back of the head (notice in halflife you can't kill NPCs, a choice I'm sure, not a flaw).
Those posting the "no personality, I can't relate" comments must find the real world a horribly difficult place. I know criminals are, simplifying here "bad". I know this not from going over and talking to them, but from their actions and interactions of those around them.
Honestly, these "no personality" comments make me think this forum has a fair few autistic children! Although I'm sure it's more just people who spend too long alone with a headset, their only means of communication yelling "take that noob", thus if the protagonist doesn't act likewise, a'la no relation. Roll-on Duke Nukem Forever and give these kids their Anti-Hero mmm-fiiiiiiiiiix!
Second point I wanted to address is the voting for text-based character such as: "my fallout 3 character". While I understand your logic (there is no sound from said character) they are not silent as the entire game has you talking to people, choosing what you want to say, using that tool to give your character a personality.
Your "Fallout 3" hero is good/bad because of the actions you chose for him and the DIALOGUE you select.
Otherwise you could go with "any character from before 1980" or we'll get Yahtzee on here telling us "Dizzy of the Dizzy's Adventures games, end of, you are all underpriviledged brat no nothings anyway so why should I care" in a very snobby tone!
I'm going to apply this same logic to characters that talk in skippable cutscenes. Just because YOU didn't listen to them doesn't make them silent, they talk, they are verbal.
Now, to give my choice:
Unsurprisingly, if you read the above Rant, I'm going for the Freeman. The games are very well crafted and well written, the character is sound (intentional pun), the character-interactions are great, the crowbar IS fun!
The others named in the list are all wonderful choices and I sit here thinking "aaah yes, didn't think of that one!"
PS. Pilot from Wing Commander anyone? Sure he sends commands via his comm-link to mother ship... but he doesn't talk... right? (I'm kind of sure I never completed the game though, so perhaps he does and I missed it) Plus, that bugger had a thousand funerals, all his friends and co-workers attended every time. It was a be-OOT-ee-fal!
(this hasn't been spelling or grammar checked, apologies!)