I liked the way the Mancubus died and Cacodaemons actually frightened me once or twice. I remember getting stuck on a level involving six or seven doors, where one has to go through each one to retrieve a key (or something like that) to move onto the next level.
The spectres and robotic spiders were fascinating, though extremely pixelated, and I loved all of it. Having to replay levels was actually fun. It didn't seem to get repetitive, because I always got better after each defeat.
'Quake II' reminded me a lot of the 'DOOM' series. Especially when you fall into boiling lava (the screaming sound effect actually made me cringe or jump) and later witness the surviving, psychologically-broken soldiers being ground into meat. Loved those games. ID Software certainly did a fantastic job! Haven't thought about those games in ages, cheers for this thread.
The strafing and such that I learned in 'DOOM' and its sequels certainly helped me when I took up 'Team Fortress Classic' and later 'Counter-Strike'; not frightening in anyway (more frustrating I'd say) but certainly fun.