"Prefer" is a strong word, but there are definitely a lot of games that I'll still play on Commodore 64 even though Amiga versions also exist. Creatures, Wizball, Head Over Heels, The Last Ninja, and Turrican II are just a few examples (that's not to say I won't also play the Amiga versions, just depends what mood I'm in).
Creatures is an interesting one because it was a technical marvel for the C64, whereas on Amiga it felt like just another game (maybe this is why the sequel only got a C64 version?).
I prefered the PS1 version of DOOM over the other versions at the time. PS1 version had that amazing soundtrack which was and still is better than the MIDI music from the other versions. I preferred playing with a controller too.
Nowadays I use a WAD file that inserts the PS1 soundtrack when playing ZDOOM or other source ports.
I'd argue that "inferior"/"better" in this case is very much debatable. Yes, the PS1 lacked some levels, monster, and detail from the original game, but on the other, it improved not only the soundtrack that you mentioned, but also replaced all the stock sounds with much nicer ones, added environmental reverb effects, and coloured sector lighting, so I don't think either version can be argued to be definitively better than the other.
I also liked how PS1 DOOM forces you to play more carefully, since you can't save your game mid-level.