There are some great suggestions in this topic (especially Daft Time)
I will give some suggestions too. By the way some of the old games have graphic/enhanchement mods, search them on google (I know especially Deus Ex, Duke Nukem 3D, Doom, Quake 2, System Shock 2)
First, some of my most favorite (Top 10) games.
- Planescape: Torment. Must to play game for every PC Gamer. Its narrative and story telling is incredible. And Its amazing world takes you into the deep. You must play this game as a mage first, up the Int and Wis, and talk to everybody around. Best game and best RPG for me.
- Sanitarium. At first this game seems weird. But after finishing the game, you will encounter one of the greatest storytelling in video gaming history. My best adventure game. Don't forget to patch the game first (you should do it in every game).
- Jedi Knight: Jedi Outcast. Jedi Knight series (including Dark Forces) is really good. You should play all the series one by one to fully understand and taste the story of Kyle Katarn. However Jedi Outcast as a stand alone game still gives much joy and experience to the player.
- Dungeon Keeper. My most favorite strategy game. Bullfrog was famous with their classic Populous, Theme Hospital, Theme Park games, they are all awesome games. However my favorite was Dungeon Keeper. It holds parody to medieval games like Diablo, but also has solid gameplay. This game has lots of detail in every aspects. I think games like Black&White, Movies, Evil Genius don't have 1/10 detail of this game.
- Vampire: The Masquerade - Bloodlines. Some people argue "only 2D isometric games can be true RPG", however this game is my second most favorite RPG. Not a sequel to Redemption, but both VTM games were very enjoyable to play. Bloodlines on the other hand, gave us theatrical NPC performances, branching story, non-linear gameplay and a marvelous atmosphere. There is one problem, you definitely must to patch it. (There are two unofficial patches, one is like an expansion pack, the other is just patches the vanilla game)
- Neverwinter Nights 2: Mask Of The Betrayer. I don't like NWN series, they are good to create your own story and play with your friends, other than that nothing awesome. However MOTB campaign became one of my most favorite RPGs. It has a very close feeling to Planescape: Torment. Thinking that new Torment game is being made by creators of MOTB...
- The Curse Of Monkey Island. Monkey Island 3 is one of my most favorite adventures, however MI1 and MI2 are also very very good games. MI1 and MI2 now have Special Edition, remade with modern graphics, you don't have to play them with Amiga graphics. Full of humor and fun. I don't suggest you to play Fourth game (didn't like it) but definitely suggest Tales of Monkey Island episodes.
- The Darkness. This game is not a PC game, console only. However I must write it here, because this game made me very emotional while playing it. I love this game. I love Jenny. I love the story. Second game was not a bad game, but definitely not great as the first game. Play it.
- System Shock 2. RPG/FPS hybrid. First game is very old and hard to play today. However SS2 is still helluva good. You may get stuck in the beginning of the game, but you will get use to it and enjoy it later on.
- The Elder Scrolls: Morrowind. This is still the best TES game. Even Skyrim can not come close to it. With some graphics update and mods, It can be still replayed on 2013 without any problem.
Other important games (you can call it Top 11-20) : Fallout 2, Sacrifice, KOTOR 2, Quake 2, Clive Barker's Undying, Commandos, Descent: Freespace 1/2, Mech Commander 1/2, Wing Commander series, Deus Ex
Some games worth mentioning: McGee's Alice, Alpha Protocol, Urban Chaos, Fallout Tactics, Arcanum, The Last Express, Heroes Of Might & Magic 2/3, Thief 1/2, Mech Warrior series, Startopia
If you played all these games, and want to play older DOS/Windows games, try these: Crusader: No Remorse/No Regret, Gods, Commander Keen, Syndicate, Another World, Beneath A Steel Sky, Jazz JackRabbit, Indiana Jones And The Fate Of Atlantis, X-Com Enemy Unknown, Master Of Orion