Well, they made doom. Other than that way back in the beginning of the 90's they attempted to make Super Mario Bros 3 to sell Nintendo a PC-ready version once they had pioneered a game engine that did side scrolling on a computer. This was the first ever. Nintendo said nope, because it would hurt the sales of the nintendo.
So Commander Keen was born.
This of course is by no means the only time they have been pioneers in creating something that hasn't been done before. Hovertank 3-D was the very first game that emulated a 3D environment.
Next in line was Wolfenstein 3-D. This one had quite a bit more detail, which by today's standards is laughable when I put it that way, but you should have seen Hovertank!
Next, they developed an engine that could read the sorroundings of a vertex (player position) and the floor and ceiling heights around it, and in a very small fraction of a second produce visually a much better 2.5D emulated 3D environment. Doom was the name. It was such a great discovery to find this game had modding capabilities and over 100,000 mods made for it to this day, because I still play the shit out of it.
If looking for ACTUAL 3-D, they pioneered it too. It's called Quake.