I recall that some of the developer commentary for either Portal or Portal 2 mentioned that they began level-development by using a special version of the namesake non-euclidean Portals to connect different chambers and hallways that were being developed in parallel.

Then, later in development, they ran a tool to stitch together all that geometry in a more-normal way, and they only had one case of impossible-overlap, which continued to use the non-euclidean link.

For those wondering where the impossible space is:

https://gaming.stackexchange.com/questions/20601/where-is-th...

I actually discovered this accidentally, because I found wheatley so damn annoying at this point, I was just noclipping through the levels to get to the next part of the game, and I couldn't noclip through that drop.

IIRC Duke3D also had a map where you had to walk a circular path twice to get back to where you started.

Duke3D used teleportation to simulate height, for instance in the beginning of the game when you drop down from the rooftop you actually teleport to a other part of the map.