Half-Life, now showing its age more than others, still comes to mind when talking about narrative/storytelling getting in the way of gameplay. The creators managed to tell a story with a silent protagonist and no text walls/cutscenes and did a phenomenal job of it.
Thief: The Dark Project and Metal Gear Solid (released mere months apart, so I kind of lump them in together) were both hugely influential in the stealth/action genre, and a huge amount of that influence is still readily apparent; Dishonored, Splinter Cell, etc. all automatically feel familiar after getting hooked on Thief and MGS as a kid.
System Shock/SS2 (admittedly 2 was a more relevant example) grandfathered in the action-RPG-shooter games that have seen a fair deal of success. System Shock laid the foundation that has given way to games like Bioshock (obviously), Deus Ex, and even Borderlands.
But who said revolutions had to be good?
Aliens: Colonial Marines, Duke Forever and Daikatana will remain constant reminders of the shitshow audiences are sometimes treated to after remaining hopeful of the end product after years in development hell.
The most specific game that comes to mind is "Spore," showcasing how far publishers (EA) are willing to go in terms of DRM, even if it does mean totally screwing over consumers.
