I have a few for different genres, and often I have two games serving as counterpoints to one another when I compare one to them - "where does it fit on the scale?" etc
Half Life 2 is an obvious one for traditional FPSes along with Bioshock for more deep, nuanced FPSs (in terms of gameplay I mean) and Serious Sam/Painkiller/TF2 if I'm comparing creative weaponry and design. Doom, Borderlands and Left 4 Dead/2 serve as my respective counter standards for those. Doom is Half Life without the compelling story, characters, weapons, environments etc, while Borderlands is Bioshock without the environmental design, and mechanical depth (though I consider neither to be RPGs). Left 4 Dead 1 showed me how variety is important to keep a repetitive task (like shooting things) fun and interesting. Left 4 Dead 2 reminds me that remaking the same game with melee weapons isn't enough to justify a sequel no matter how much Valve wants me to believe that, and helped kill any interest I had in murdering zombies.
I tend to use the fallout series as my standard for RPGs with the Mass Effect series for character interaction and specifically Mass Effect 2 for things like combat in RPGs. A special mention goes to Deus Ex for epitomizing that kind of "here's a situation, tackle it however you want" gameplay. Mass Effect 2 does however write the book on how to fail at a main plot, making it railroady, insultingly stupid and canon-breakingly irrelevant to the series overall arc. Morrowind is the opposite of Fallout, serving as an example of a game that, no matter how how expansive it's world is, can still shut me out completely if it's gameplay is useless. Fable is similar in that it taught me a valuable lesson about how role playing can't be boiled down to 'good' and 'evil'.
Psychonauts is my gold standard for creative, funny dialogue and imaginative scenarios. and Mirror's edge is my pick for how first person games should function, even if it was a bit rough around the edges. I contrast that to any given gamebyro game which couldn't make me feel more like I was playing as a camera with a gun. Penumbra: Overture serves as my pick for both horror and physics integration to which I contrast Doom 3 and again, any gamebyro game. In terms of story however KOTOR and in particular KOTOR 2 serve as shining examples of how to deconstruct an otherwise simple and black and white universe in an interesting way. Warrior Within was not.