I've been lost in too many levels for me to say, I can't remember working out progression of the levels back in the day (mainly because I'd always be noclipping around the maps, and had walkthroughs even back then), and of course Final Doom scrambled my brain up even more, but I do remember one thing: first playing E1 on the SNES port, my first play I overlooked both the optional maze in E1M2 and the optional yellow key area in E1M3, just would've strolled past the entrance to both, because on my second (or even third) go I was like "whoa shit, I missed this area".
But yeah, also agree with the others about Command Center/Unholy Cathedral/Gate To Limbo/Downtown/Chasm/Spirit World. Fuckin Petersen.