PC Gamer UK at least used to have a top 5 list of the best games in every genre included at the back-pages of every magazine. For a reference point, I looked up one magazine from 2000 to check out what they liked at that time. Red Alert 2 was at the magazine cover, Star Trek Voyager: Elite Force was the game of the month with a 92% review score, same as Red Alert 2, with Sacrifice also being rewarded a nice 90% score and Age of Empires 2: Conquerors and Cleopatra and getting 86% and 84% respectively. There was also a whole bunch of review scores ranging from 20% to 60%, which I guess you don't see much nowadays. There was an article about horror in games which praised Return to the Cathedral (from Thief: The Dark Project, duh) as the scariest level ever created. They re-reviewed some older games, giving Dungeon Keeper 2 the score of 80%, Unreal Tournament 91% and the first Quake 75%. There was also a page for reader reviews, where some wimp gave Soldier of Fortune a score of 36% (original score 86%) and some moron thought that VtM: Redemption was a 96% game (rated 70% originally).
Anyway, here's a couple of the top 5 lists found at the back (it should be noted that the magazine didn't exist until 1993, so games from before that are not in save for one or two exceptions):
FPS:
1. Half-Life (96%)
2. Quake II (96%)
3. Aliens vs. Predator (90%)
4. Star Trek Voyager: Elite Force (92%)
5. Delta Force 2 (86%)
Action Strategy:
1. Hidden & Dangerous (93%)
2. Sacrifice (90%)
3. Battlezone 2 (93%)
4. SWAT 3 (91%)
5. Abomination (89%)
RTS:
1. Shogun: Total War (92%)
2. Earth 2150 (91%)
3. C&C2: Red Alert 2 (92%)
4. Ground Control (87%)
5. Age of Empires II: The Age of Kings (90%)
TBS:
1. Civilization: Call to Power (92%)
2. Alpha Centauri (91%)
3. X-COM: Apocalypse (93%)
4. Age of Wonders (87%)
5. Star Trek: Birth of the Federation (88%)
Action Adventure:
1. Thief II: The Metal Age (89%)
2. Outcast (90%)
3. MDK 2 (88%)
4. Urban Chaos (88%)
5. Indiana Jones / Infernal Machine (91%)
Adventure:
1. Monkey Island trilogy (94%)
2. Grim Fandango (95%)
3. Sam & Max Hit the Road (93%)
4. Broken Sword 2: The Smoking Mirror (88%)
5. Day of the Tentacle (90%)
RPG:
1. Deus Ex (95%)
2. System Shock 2 (92%)
3. Baldur's Gate (89%)
4. Diablo II (90%)
5. Final Fantasy VIII (92%)
All in all, it's a mixed bag. Pretty much all of the #1 games are undisputable classics of their own genre, but going further down the lists it gets a bit weird, with some garbage (FFVIII), some strange omissions (the Rainbow Six games, non-LucasArts adventure games in general), and just some plain weird choices (Birth of the Federation). You might notice that three games from the very same issue can be found on these lists (RA2, Sacrifice, Elite Force), so there's probably a lack of perspective in there, if not outright bias towards newer games. The genre definitions are also a bit iffy (action strategy, DX and SS2 topping the RPG list...), but I guess that kind of stuff is inevitable if you want to make strict genre-based lists and still include all the best games.
Of course AAA gaming still hadn't completely devolved into shit in 2000, so making up terrible lists was harder back then, but just looking at some of those titles makes it once again obvious how hard the decline has struck.