PC

This is a tough one.... it will probably change depending on my mood.

Overall:

1 - Dark Souls
2 - XCom Enemy Unknown
3 - The Walking Dead (Telltales)

Exclusives:

1 - Mechwarrior 4 Mercenaries
2 - Papers, Please / This War of Mine (Can't decide...)
3 - The Stanley Parable

Diablo 2
Descent 2
DayZ mod

System Shock
Sid Meier's Alpha Centauri
Ultima 5

I feel like I should mention Fallout because it's practically tied with these for me.

Binding of Isaac
Diablo 2
Bioshock 1

If we are talking exclusives

Command and Conquer Tiberian Sun
Total Annihilation
Caesar III

Also, throwing in a bonus couple games that people probably haven't heard of or even remember:

The Incredible Machine
Super Solvers Treasure Mountain
Mixed Up Mother Goose
Duke Nukem 1/2

And pretty much any game that was released on the 5 1/4 inch floppy disc in the style of Jane of the Jungle.

Exclusives:

1.) Baldur's Gate (the original; I haven't played the Enhanced Edition)
This single-handedly got me into the world of PC role-playing. The scope of the world and what you could do in it as a player was unmatched by most console games I'd played at the time. It's still a blast.

2.) STALKER: Shadow of Chernobyl
Most FPSes I'd played before STALKER had largely been corridor-based affairs, but STALKER offered a truly open world before the phrase "open world" really entered the gaming vernacular. Toss in a twist of sci-fi and survival horror, and you had a real unique FPS experience that still stands today.

3.) Command and Conquer (Tiberium Dawn)
This, coupled with Warcraft II, game got me into turn based strategy gaming. Despite being a really early offering in the TBS genre, the game hit all the right notes, with factions, units, balance, and so on. The AI could be unfair at times, but you could always sandbag your way into the middle of the enemy base and set up an Obelisk of Light to even the score. The story, with the campy, live action cut scenes also really stood out at the time, and made war fun. Kane is still one of my favorite characters in gaming.

---

Multi-platform Games:

1.) Deus Ex (This was also on PS2)

2.) Half Life (This was also on PS2)

3.) Diablo 1 (This was also on PS1, and took up 10 out of 12 blocks on a standard memory card!)

---

Honorable Mentions:

Fallout 3

Elder Scrolls III: Morrowind

Doom 2016

Tomb Raider 2013