Yeah, I'm not including RPGs with non-existant stories, because there are quite a few of those, and you can't fault a game for something that it doesn't even try to have.
I would disagree with Fallout 3, completely. When we talk "story" in RPGs, we're usually talking about the all-encompassing narrative elements, this extends to setting, style, plot, dialog, characters, etc. Fallout 3 is probably best known for it's setting, style, and fun non-linear dialog. I wouldn't say it's particularly lauded for it's gameplay, though that's not bad. And I would hardly say that there's even anything particularly bad about the story, besides the ending. All of the other games in that list I've heard positive comments regarding some section of the narrative, even if the main focus is on gameplay.