Certain early 3D titles, even if their main characters are polygons, tended to use sprites for certain common object placements like items or small enemies, typically as a means of keeping the visual clarity of a far-away object without using any excess polygons; see Chameleon Twist. It was also really common back then for sprites of colored spheres to be used in tandem with other sprites or polygons to create certain characters that have rounder and more simplified body types. Many of the characters and objects in Bomberman 64 seem to be a good example of composite characters in action, and I believe many enemies in Kirby 64 and Super Mario 64 follow this method in well. Only other good example I can think of is Paper Mario, and they specifically amplify the "2D" nature of their characters by literally flipping them like paper whenever a character turns direction. Technically valid, but it's a different feel.
Outside of that, it seems to be pretty rare outside of the Doom space. Largest contributor to this is probably the fact that making multiple animations in 5-8 angles that are high enough quality to be considered "acceptable" is kind of a nightmare unless you're condensing a lot of the animation work that would be necessary in some way.
Some of the WayForward games, specifically Ducktales and Shantae, could be considered on the list, and Bug Fables' visual style is roughly the same as Paper Mario's. That's all I can think of for recent titles.