Struggling to come up with anything not here. But I remember a doom-clone with anime(-ish?) graphics on PC. I just remember an article about the animes. Maybe it’s already in your list.
Dunno if this has anything extra: https://www.doomworld.com/vb/doom-general/68548-full-list-of-doom-clones-similar-games/
Copied the list over to ol’ doom-clones page on the wiki BTW: http://wiki.selectbutton.net/genre:doom_clones
some of the doom community guys did an original game using the zdoom engine for a game jam, i don’t know if you count this but hey! i played it awhile back, it’s decent and goofy
i think this is now the most complete list on the internet, and there’s still more work to do.
also, wtf, give me some bloodpotions i’ve spent mad hours on this thing 
first space hulk is dungeon master-style cardinal directions movement.
Are games with FPS segments accepted? For instance, half of Ice & Fire is on-rails sections, and the other half is the FPS bits.
of course! lots of these games have just segments - for ice and fire, how would you describe the FPS segments without using the term FPS? (e.g., for Jurassic Park SNES i put “building interior mode”)
and ice & fire is on the list now, anyway
seriously i haven’t slept i’ve just been researching this for hours
I liked this one a lot back in the day. As a bonus, the video includes the FMV mission intro
The PC/Mac versions of these games used polygons, but they were demade with sprites on the SNES
Pretty sure the same thing happened with Wing Commander but I’m not sure if those kind of games are being included?
Oh, and of course the SNES had Super 3D Noah’s Ark but that was unlicensed.
Also this:
this is good, i can’t make any more edits for 10 hours though because i broke discourse
I had no idea there was a SNES port of Spectre. How absolutely bizarre.
oh god, you’re starting to go deep now, truly nightmarish stuff
aw man i was totally gonna post about clone the first time i woke up this morning, but then i fell back asleep and forgot about it
Apparently Chex Quest 3 saw an unofficial release from the former lead artist of the game:
http://www.chucktropolis.com/gamers.htm
It’s very unclear, I’m not sure if he made it from scratch or what!
Tatsumi’s 1986 arcade game Lock-On is gorgeous but does not allow you to turn around - quite a few games like this out there
80’s amiga games with not enough sprites to count, but incredible nonetheless
these games are so good, again not enough sprites but captivating