I feel like there wasn't really a single golden age for PC gaming, since each genre has had its own golden age. Doom, Duke Nukem, Unreal, and others probably comprised the first FPS Golden Age, but that was happening separately from other Golden Ages that were happening. You also had RTS games, Strategy games, and a bunch of other PC genres.

As far as when that first FPS golden age ended? I'd almost say that 1997's Goldeneye 007 for the N64 marked the "end" of the PC FPS golden age, since that's when console gaming got its first big exclusive FPS hit. EVERYBODY I knew was playing that game when it came out and you just couldn't play it on the PC at that time, it marked a shift from PC to console gaming. Some genres would never make the jump successfully, like RTS games, but FPS games and Adventure games seemed to work well and that's where all the cool new games went to. Obviously consoles had had hits before this, but that seemed like the first time they got something above and beyond just Mario or Sonic-style platformers.