Fair enough lol. Not all 3D gaming obviously (I mean they aren't First person shooters, like most of your examples), but effectively the Action, Adventure, Platforming, etc angle (which makes up a fairly massive chunk of games today).

What I'm talking about is the fundamental gameplay of both. Online Multiplayer was revolutionary, but it wasn't really a fundamental change to the gameplay itself (Like with Marathon introducing mouse control)

It's interesting that you mention Tomb Raider though because that's a perfect comparison. It was a fairly indicative of the industry as a whole with its stiff controls, static cameras, and dodgy combat.

Mario 64 brought a full range of movement and action to games. It was really the first 3D game where just moving was fun (which is why they started the game in a peaceful courtyard, they wanted you to just have a fuck about). It also brought the user controllable camera to games (It hasn't aged well, but that camera system was amazing when it came out). Also, while it didn't invent the Hub world (it had been used in 2D games) it pretty much set the standard for it.

OoT built on Mario64 with two major bits of gameplay. Target lock-on (Then called "Z-Targeting") and contextual buttons. Both of which are just so fundamental to games these days it just feels obvious. More relevant back then (but not now), it created the template for how you could faithfully transition a series from 2D to 3D while perfectly maintaining the feel of the 2D series.

Now, neither of those things alone would justify it being in my Top 5. The fact that they're both so aggressively fun and well made does that.