Quake, no question, GOAT FPS - invented the modern FPS industry - responsible for the rise of PC gaming IMHO - killer app for the Pentium and subsequently the Voodoo - the online gaming community and the modding community - levels were very balanced and there was a giant return on skill increase - i.e. the more skill you got, the more it showed - rare for modern FPS to be that way where they dumb things down so everyone can get a kill or two even if they suck
BTW - Quake code is still used in Call of Duty
I'm curious to know how the Nintendo vs. Sega vs. Sony fans divide in terms of their support for either FPS and which one they preferred... My rough sense is that most Nintendo fans preferred Quake and most Sony fans preferred UT - I found most Sega fans split down the middle - but I have no real empirical basis to make that claim outside of what I observed among my friends that owned PCs during that era and what console preference they had