Speaking for myself I will say that I oddly enough own his top three games.
Truthfully I will also say that "Just Cause 2" seems like a pretty consistant choice from him, because it's a decent free roam game, with a lot to do, and a fairly irreverant attitude. Looking back at his love of "Saint's Row 2" (which I agreed with him on) I can see how this was his pick.
I think "Just Cause 2" would have benefitted from letting you design your own agent (like you could you criminal in "Saint's Row 2"). I also think it could have used some sex in there with all that wonderful violence and destruction.
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Amnesia is kind of "meh" from my playing it so far. I think Yahtzee rated it so highly simply because it's one of the very few attempts people have made to make a game that wasn't just a glorified shooter. Sort of like how he rated "Grand Theft Auto IV" fairly highly but then recanted it by saying that he was so let down by gaming as a whole that he was looking for any glimmer in the then-stinking morass of developed game, and it simply got a reasonable review by being less-bad than what else is out there. Amnesia sort of gets a high rating by default for being one of the only actual horror games anyone tried to develop.
That said, as far as the type of horror involved, I will say that the game is definatly kind of low-brow. See, the whole "the best horror is what people create in their minds" bit is what is done for the masses, people that can't deal with being really unnerved or offended by someone. It's the kind of horror you see most in mass-press writing for the casual reader like what Steven King puts out, especially nowadays. It appeals to the masses, but by their nature the masses are hardly an intellectual elite.
Smarter and more "hardcore" genere fans have the issue of usually being quite jaded, and also have a firmer grasp of reality and tend to be harder to get into a mood of suspension of disbelief. The mark of a serious horror creator is someone who can come up with a concept that is going to take that guy who is sitting there expecting horror and saying "okay, scare me, Lol!" and be able to come up with something inspiringly freaky or shocking, above and beyond the occasional 'jump out scare'.
Amnesia is kind of a "by the numbers" approach to horror, I'd rate it as being solidly average, well told, but really not much that hasn't been seen before. I also think the lack of any combat elements is kind of a crutch rather than a feature. The issue being that I don't think many developers can achieve the middle ground needed to have a combat element without turning the game into a shooter. Games like "Resident Evil" and "Silent Hill" got it right, and I think part of what made those games classics of the genere was that through arming the character in going out to deal with these things, he/she was behaving like a normal person would under such circumstances. While not smooth the combat mechanics reinforced the horrific nature of the game, and the capabilities of the enemies as much a anything and encouraged you to avoid confrontation, while at the same time not making it entirely nessicary. In Silent Hill Or Resident Evil, you might be able to "buy your way out of a problem" through combat (which makes sense) but there simply aren't enough resources to do that everywhere, and using those bullets (which are finite in supply) here, means you won't have them for something worse later. Thus in cases where you have an option, your going to find ways to get by the monsters without using your weapons above and beyond anything else.
All the praise for a lack of combat seems to be misplaced in my opinion, I tend to think it was more a matter of them not being able to come up with a compromise that worked (like many classic horror games did) rather than a major design desician.
I can see why it's on Yahtzee's list, but I also can't shake the feeling that it wouldn't be there if we simply saw more quality teams working on horror games. With the guys who did "Silent Hill" working on absolutly abyssmal "Saw" movie tie-in games, and Capcom being some of the worst offenders in the "let's turn our horror titles into shooters" crowd, and a lack of interested developers in general... well I think it's one of those "any port in a storm" situations.