Ocarina of Time certainly fits the bill for a video game masterpiece. It revolutionized gaming and established so many tenants of modern 3D gaming which are fundamental mainstays today.
Virtual Camera Control
Six Way Analogue Directional Movement
Cutscene Rigging and Cinematography
Lock On Targeting and Aiming
Contextual 3D Environmental Interaction
It didn't just establish these modern mechanics for a new technological era in video games, it executed them flawlessly while presenting an epic, entertaining, and meaningful gameplay experience in its own right.
Thief: The Dark Project was the Ocarina of Time of the personal computer. The narrative storytelling, 3D environmental technology and sheer brilliance of its level design was the future of video games. An honorable mention goes to Deus Ex for its similar impact at roughly the same time.
By far the most underrated gaming masterpiece, however, is Cyan World's enigmatic Myst and its sequel Riven. Myst absolutely blew up the gaming scene back in 1993, where it sparked something of a cultural revolution in gaming, drove hardware sales on its popularity alone and brought non-gamers into the fold with its ease of use, accessibility and advanced presentation. Myst is largely responsible for the wide spread adoption of the CD-ROM drive. Mainstream media sources wrote pieces on the phenomenon, making it one of the first video games to garner wide spread attention amongst the non-gaming demographic. Finally, non-gamers were seriously discussing the potential of video games as an art form. While its Hypercard technology slide show presentation didn't technically make it a real time 3D engine, Myst's 3D graphics were beyond what any other game had achieved at the time.
But what Cyan had established with Myst, they refined and cranked up to 11 with its highly anticipated sequel, Riven. While Myst's narrative seemed somewhat incidental, for Riven Cyan's storytellers took to creating a fully fledged, believable world, character histories, and the real beginnings of a fully fledged mythology. If Myst's graphics were profound, Riven's were absolutely gobsmacking. The photorealistic imaging Riven accomplished is even unsurpassed to this day among some AAA titles. Myst's puzzles were engaging and challenging, but Riven's were absolutely fiendish, and all of them were integrated believably into Riven's living breathing world. More than anything, Cyan crafted a real world with Riven, rendered down to the finest detail. And the narrative on display, with its largely visual storytelling, advanced nonlinearity, heavy themes and astounding circular structure that even ties back into Myst are utterly brilliant. And the soundtrack is one of video game's best.
Myst represents an alternate evolutionary path that video games might have taken, but that unfortunately largely ended with Riven. The popularity of today's "walking simulators" don't hold a candle to their illustrious predecessor. Myst and Riven are one of gaming's most prolific "what-could-have-beens." They were trend setters that made a massive impact, but sadly the effect they had on video games hardly resonates today.