Almost ate my gum on that one!

HL2 and mute Freeman works for me. Because I am (the) Freeman! :)
Or maybe its because i grew on Wolfenstein 3D and Doom...

I hated Gordon's inexplicable silence in the Half-Life games. It's clearly meant to be a story-driven game--even to the point of having awkward, half-hearted pseudo-cutscenes--but Gordon says nothing. Some characters even try to hold some form of a conversation with him, which makes it all the more laughably bad. I can accept this in a game like Zelda, where the story is there to complement and make sense of the action (rather than the other way around), but with the Half-Life series it's clear that the developers were trying to come up with an interesting setting and plot to embellish a game that is otherwise comprised of mediocre FPS-on-rails combat and ultra-linear level design.

On the other hand, you have games like Final Fantasy X or Tales of the Abyss where your character's voice is so excrutiatingly obnoxious, that it's hard to put up with the game.

That's a very interesting topic. I think there is a difference between emphasizing with a character and actually taking on his personality. I don’t think the latter ever happened to me, in either a book, film or game, and I’m not sure that what the article describes is actually what Valve is striving for. What Half-Life did for me by removing a pronounced character was removing an obstacle between myself and the world Valve had created. Gordon never functioned as a slot for my personality, so if that was their intention, it didn’t work for me. The whole silent protagonist thing really did however, in a way, allow me to see the Half-Life world through my own eyes, since it was not filtered through a strong character. I hope that makes sense.
Half-Life 2 really worked for me, but I’m not sure how much of this has to do with Gordon’s non-personality. The game is simply better written, has more interesting characters and a more… pronounced artistic vision, for lack of a better term, than nearly everything else out there, so perhaps that’s the deciding reason I liked it so much. Perhaps I would have liked it even more with an interesting character.
Bioshock for example only bored me, while I loved Portal, another game with a silent protagonist. So… I really don’t know. As for Role Playing games, I never play myself, always an imaginary character I imbue with certain attributes.
Yeah, the concept of a player really thinking himself into a video game character is iffy. Part of that is probably that every game allows only for a few predefined possible actions, so the player can never really naturally unfold in such environments.
One last thing… I don’t agree that JC Denton is a well-developed hero. For me, he is much closer to Gordon Freeman than to Duke Nukem.

Well, in Bioshock, noone speaks directly to you and expects an answer back (as I recall, although I haven't played it in a very long time). In Portal, the only one speaking to you is so obviously bat shit insane and out to kill you, that talking would be a pretty futile exercise. Also, the protagonist in Portal is completely anonymous. I think she has a name, but the game never mentions it, and there is nothing in the game that defines her in any way. I think the same might be said about Bioshock, but again, it's been a very long time and I can't remember.
Gordon Freeman however, is not anonymous. We know tons of stuff about him, and the Half-Life games (especially from HL2 onwards) are full of things that relate directly to him as a person. He has friends, enemies, allies and even a potential love interest, that all speak directly to him at various times, and carry on conversations involving him, and he ignores them all completely. Apparently the guy can't put together a coherent sentence, and he's supposed to be a physicist, as well as an all-round hero. It worked sort of okay in HL1, but from HL2 onwards it felt completely unnatural.

The voice acting, animation and writing of the NPCs is most likely what made it work for me. I always got the impression that Gordon is talking, we just don't hear it.
The whole thing also added an enigmatic touch to the games, just like the fact that a lot of the story elements are never explained to the player. But that's probably something else many people don't like.

Her names GLaDOS
"What Half-Life did for me by removing a pronounced character was removing an obstacle between myself and the world Valve had created"
thats exactly how i feel about it.

Personally, I never felt like Valve's decision to keep Gordon silent was ever to immerse the player. I think it's more along the lines of he doesn't really need to say anything. Adding dialogue in for the sake of dialogue would result in cheesy one-liners, completely destroying his character. In a way, I think his silence speaks volumes about his true character.

Glados was the name of the computer AI in charge of the portal facility, not the silent protagonist. I don't believe they ever gave her a name, not even off camera.

Yeah, it's a very dramatic and serious game, not Duke Nukem.

I prefer characterisation. Its not like everyone who uses a gun for a living is a frothing neckless cretin with less mental capacity than a dead mouse. Despite the circumstantial evidence to the contrary, it is possible to have someone speak and not be a macho dick

The female protagonist in Portal is named Chell.

Apparently her name is Chell but I have no idea where that's communicated in game. Presumably its not but was mentioned by the devs which is why it seems official. Going purely by the game, we'd have to assume she's called SUBJECT NAME HERE