Though I love both games, I've always preferred the combat in Quake 1 to Doom, and it's because the enemies all felt far more dynamic. The first time I encountered and ogre in e1m2, it kicked my ass because I was so unaccustomed to early enemies having that much health, because I was in the mindset of Doom and it's many cannon fodder enemies. There were a few levels in the base game that were just a pain in the ass though, specifically e2m4 and e3m4 because of some real cheap enemy placement.
It was the custom maps that really cemented my love for the game though, because so many of them just perfect what the original levels were attempting.
My favorite custom map is The Masque of Red Death, probably one of the fairest slaughter maps on offer in Quake 1.