I love to talk about Portal and BioShock together because I think they are great for the same reason. It's not the dry humor of GladOS, the moral quandary of harvesting ADAM from little sisters, the novelty of creating portals, wielding a swarm of bees, or having tape recorders sharing history. Each of these elements was amazing and should not be underestimated, but what made each games so much more was the power of the emotional mirror between the experience of the player and their avatar.
Both games embrace -- or at least stumbled upon -- what I believe is a particularly potent narrative arc when told through the gaming medium: that of escaping enslavement and seeking revenge against the enslaver. In Portal, that moment coalesces when you are descending into the fire pit and GladOS is saying farewell and you use your portal gun to make it out of the situation. In BioShock, it the moment when you discovered and escaped your enslavement, with the phrase, "Would you kindly..."
The reason this narrative arc is so well-suited to games is because it so mirrors the emotional setting of every gamer, wherein a player (avatar) attempts to survive the machinations of the game designer (GladOS, Andrew Ryan). The reason why escaping the fire pit in Portal and the beating of Andrew Ryan in BioShock carry so much emotional release is because the player gets to turn the tables on the game designer, becoming free to do as he or she pleases.
This freedom might be an illusion -- you may remember BioShock becoming a bit of a slog after Ryan's death (the extra work following erodes the idea of having defeated the designer, no?) -- but I believe the power of both games is due to this particularly formidable gaming narrative archetype. It might be fun to attempt one day.