1.) Narrative/Story:
Planescape Torment - What else should I place?
Deus Ex - No explanation needed.
2.) Exploration/Ambience:
Gothic 2 - It's a shame how very few of you mentioned this gem. Aside from challenging combat (which becomes easier on your next playthroughs) Gothic 2 fixed most of the problems with the first game while retaining what made the first one great like exploration and RP Elememts.
Dark Souls - Other than being a 3D Metroidvania, I love the quest design. Instead of having the usual "come here to get a quest" dialog option for
NPCs, Dark Souls' quests are activated by the moment you talk to the NPC but they are invisible to the player; that isnt what makes the quests here great thou, what makes them great is how they are progressing as the player progresses in the story and can only be completed by interacting and exploring the game world(or by walkthroughs). An example is Siegmeyer's quest which can be read here: http://darksouls.wikidot.com/siegmeyer-of-catarina. Most of them are grey when it comes to C&C and make the world feel more real and immersive.
Morrowind - Morrowind is one of those few RPGs that managed to combine two subgenres of an RPG: the Dungeon Crawler and Adventure RPGs. Despite a smaller world and weaker character creation than the previous 2 TES games, Morrowind makes up for this by being more polished and blending the Dungeon Crawling focus of Daggerfall and the Exploration focus of Gothic. The magic system here is also amazing and the quest design is great.
3.) Choice and Consequence:
Fallout 1,2 & New Vegas - They are here not just because of their C&C but because of how the stats affect them. In the Bioware RPG like ME and BG, the stats have very little effect on C&C other than the occasional Intimidation/Persuasion check and the endings; in Fallout however, stats affect the role that you play. The choices and their respective consequences available are dependent on the role you want to play, which makes Fallout an RPG with actual role-playing instead of just stats and a story.
Vampire the Masquerade Bloodlines - It's a Troika Game, Troika usually have better C&C than most RPGs out there.
4.)Strategy and Tactics - Any RPG that revolves around strategy and tactics alone isn't an RPG. X-Com and Fire Emblem arent really RPGs but strategy/tactical games, thou one can argue that the lastest installments in both games are RPGs, but I digress.
The RPGs with the best strategic combat imo are ToEE, Jagged Alliance 2, and DOS 2.
5.) Character Creation/Progression:
Fallout - reason stated above.
VtMB - I may sound like a fanboy but Troika games tend to have actual Role-Playing more than most RPGs. VtMB's Character creation is the only thing that could rival Fallout's, IMO. Also unlike most RPGs, the race you pick in VtMB could alter your whole experience of the game especially if you pick a Malkavians or Nosferatu.