I've had the exact same experience. Every time I boot up SM64 or OOT everything looks so blocky compared to how I remember it looking as a kid, it momentarily surprises me every time. In my memories the graphics are on par with AAA games now.

Picked up a Vive a few months ago--Valve created a program for it called Destinations where people can upload 3D environments with optional simple animation triggers, and you can teleport through the environment in VR. Somebody uploaded the exterior of Princess Peach's castle and the Shadow Temple boss area to it. Checking out Peach's castle in the headset was breathtaking, got that same kick to my chest and feeling of wonder I remember having as a kid and felt like I really recognized the environment in a way I didn't when I booted the games up in emulators. Being there in VR made the graphics look worse--the tiny textures originally meant to be viewed on a CRT get blown up across the several literal football fields and the polygons are huge sharp edges several feet across for the hills. I'm not sure why it provoked that emotional response in me. I would guess that I felt more immersed, and that immersion affected my perceptions as a kid.