Godot

I mentioned Spyro's skyboxes (also used for portals+seamless level transitions), but it also used VC for the textureless LoD models which allowed incredible draw distance for the era. Random effects mostly resulting from flame breath (soot, glow) but also some other small details (like the level boundary headbutt effect). Lighting too (more obvious in the worlds with bonfires).

Also Crash Bandicoot. Here's a video on the character design (the vertex animation and spin model is interesting as well).

VC might not be obvious especially when it was just an optimization, though it might be more obvious if it used for a specific effect (like transparency), especially when viewed with modern resolution (+unfiltered textures).

Lots of games from this era have vertex lighting (and it certainly is a cool aesthetic* on its own) but I am much more interested when it's actually used to significantly reduce texture usage (plus introducing other benefits). In-engine cutscenes and midi soundtracks (or stuff like sfxr) are also good for similar reasons.

* Will be nice to try it when 4.4 finally drops (it re-adds per-vertex shading) especially as it is an actual optimization. I say this as someone who turns pixelation filters off.