One can take two approaches when making a list of the best of all time. Either one evaluates the game for how they were when they came out, or for how they are when played in the present. I've taken the latter approach - which means that games that I played to bits back in the day (Dungeon Master, Heretic, etc.) does not make the cut. There are still plenty of older games on my list...
The other big point is that this is my personal list. Firstly, it reflects my tastes - I'm a big fan of roleplaying and strategy games. Secondly, it also reflects to what I've gotten around to playing... there are many excellent games out there which I just have not played yet.
1. Civilization V (with both expansions, 2013) - the latest and greatest in the Civilization series. I spent several months playing only this game. For 40-60 hours per week. It was an addiction, and I expect I shall return to it... the only disadvantage being that it engulfs me to the degree that nothing else gets played... or done.
2. Morrowind (with both expansions, 2002) - the apex of world building in an open roleplaying game. Unique, quirky, hostile, first entering the island of Vvardenfell was a unique experience, and with mods, still holds up to this day.
3. Neverwinter Nights 2 (2006) - Obsidian's best work so far, and with the incredible character building freedom of D&D 3.5. A great adventure to explore, lots of companions to meet and interact with. Where the Elder Scrolls series is built around utter freedom for where you go and what you do, this gives you utter freedom for who you are, what your character is and can do. Supposedly, Mask of the Betrayer is even better than the original campaign, but I haven't played that yet.
4. Skyrim (with both expansions, 2011) - the gameplay and character development breaks free and finally gives you the freedom to play as you want without worrying about your character being underpowered. The world of Skyrim, while not as unique as Morrowind's, is still an engrossing and beautiful place, filled with discoveries, things to do and places to see.
5. Thief: The Dark Project (Gold, 1998) - created a genre (together with Metal Gear Solid, which came out the same year), and has superb level design. Each level is a puzzle, but offering multiple solutions - you are very free to choose your own path and way to attack the level, with very little handholding. Also has superb atmosphere, and with mods, holds up very well (I am currently playing it, and it is as good as ever)!
6. Pharaoh (1999) - the best city builder ever, and the height of Impressions Games' city building series. Adding to the city layout, people happiness handling, and manufacturing chains of its predecessor, this had the giant monuments of Egypt - pyramids that took decades of in-game time and hours of real-time to build. Successful cities looked beautiful, and the interface had a great selection of overlays to analyze your city with.
7. Titan Quest (2006) - my favourite action-rpg. I've always found randomly generated dungeons to be dull and generic, and have preferred carefully hand-crafted worlds - Titan Quest offered this, along with a great-feeling combat system, and unparallelled in the genre freedom in character building, due to being able to choose two specialties and combine them. Really looking forward to its spiritual successor, Grim Dawn.
8. Rise of Nations (2003) - creates a compressed real-time strategy experience out of Civilization. Playable in half an hour - or much longer, depending on how one sets up the game - going from ancient history up to nukes, and with plenty of nations, each with slightly distinct flavour. Also, still looks surprisingly good for its age.
9. Oblivion (with expansion, 2006) - while not as good as its siblings, as it went for a too typical medieval fantasy, it still provided a world to lose oneself in, and lots of hidden stories and treasures to find, and mods to enhance it further.
10. Angband (or variants thereof, 1990) - my roguelike of choice, the Angband family has always been more focused on highly tactical combat, and less on knowing spoilers, than its Nethack, Adom, and Dungeon Crawl brethrens. The strong focus on clean open source-code, starting with Ben Harrison's period as maintainer, has led to a plephora of variants, many of them great games in their own.
11. Alpha Centauri (1999) - the only strategy empire-building game where a fictional setting has felt as rich and immersive as mankind's real history. And gameplay-wise, was very innotative, including some things sadly not seen again since in the main Civ series, like the manipulation of terrain height, or custom building units. While the interface is clunky, the game works fine at high resolutions and looks okay.
12. Railroad Tycoon II (1998) - the best economic strategy game ever, allowing all kinds of tactics to manipulate the stock market and your competitors. Play it straight, build a sound company. Or go heavily in debt, then dump your shares and the company. Short-sell your opponent's stock to drive the price down. Just beware the margin call! Plenty of scenarios, with a high variety of objectives, kept it fresh.
13. Dungeon Siege 2 (with expansion, 2005) - an action-rpg with a difference, as one controls a party of four instead of just a single character. This allowed a very wide variety of builts - from very focused (e.g. 3 mages, focusing on different elements + 1 healer, or 4 summoners) to the more traditional balanced mix. The expansion's two new hybrid classes opened it up even further, and with the option to pause and give orders, battles are quite strategic in nature.
14. Shadow of Mordor (2014) - so many game systems all working well and coming together to create something extraordinary. Combat feels great, whether melee or ranged, stealth works well (though Far Cry 3 has even better open world stealth), the two world maps are beautiful and filled with activites, and the ingenious nemesis system ensures there is always more stuff to do.
15. Shadowrun: Dragonfall (Director's Cut, 2014) - old-school roleplaying game in the unique Shadowrun settings (Cyberpunk with Orcs, Dwarves, Elves, Trolls and Dragons). Excellent writing, interesting turnbased battles, and a great story all makes this a game that I was delighted to help exist through kickstarter.
16. Dishonored (2012) - while the stealth does not live up to Thief's or Splinter Cell's, stealth is only one possible approach here. It's the freedom - wide open levels with a multitude of paths through them, lots of supernatural abilities to choose from - that makes this game superb. I played it once, and am planning on playing it again, but going for a different style, different abilities, and different story choices - it will be a very different experience, and that is the strength of Dishonored - the freedom, the breadth of it.
17. Bayonetta (2010) - the apex of the Devil May Cry-eque hack'n'slash genre. Crazy, beautiful, challenging, and very rewarding to learn its combat system. The fact that the sequel is a Wii U-explusive is enough to tempt me to get that console.
18. Blood Bowl: Chaos edition (2012) - strategic and violent fantasy sports. While the implementation is clunky at times, the sheer quality of the underlying board games rules (ranked in the top-100 on boardgamegeek) shines through, and with 23 different races to choose for your team, and multiple ways to develop any of them, it has almost endless variety. Despite my fear of online gaming against real people, this game drew me in enough that I put up with the occasional troll and rude person, just to be able to enjoy this eminent strategy challenge.
19. Tomb Raider (2013) - while I wish the Tombs had been larger, and with more challenging puzzles, I loved the rest of the Tomb Raider reboot - the traversal puzzles were great, combat felt satisfying, and the open areas and survival elements were fun. The occasional too tightly scripted sequence did not prevent me from enjoying the game immensely.
20. Icewind Dale (2000) - where Baldur's Gate was a sprawling experience, Icewind Dale was tighter and more focused. Being linear allowed battles to be better balanced and more challenging, and building your own party of six characters from scratch gave great freedom to the player to set his own composition and strategy. Also, the cold vistas of the Icewind Dale were the most beautiful ones of the Infinity Engine games.
21. Dark Messiah of Might & Magic (2006) - first-person melee combat never before (or since) felt this visceral and satisfying. Add in a fairly deep magic system, and stealth elements, and you have an adventure that allows many playstyles to bloom and all of them feel satisfying. While Arkane's next game, Dishonored, greatly improved on level design, its melee combat could not live up to Dark Messiah's sheer intensity and satisfaction.
* Far Cry 2 (2008), Far Cry 3 (2012) (both excellent open world games... where Far Cry 2 is the more immersive by far, but Far Cry 3 loses some of the more tedious repetitive elements, and has the best open world stealth I've played)
* Gothic (2001) (such excellent gritty world building, a much darker feel than the Elder Scrolls or typical D&D)
* Hearthstone (2014) (addictive and accessible)
* Jedi Knight 2: Jedi Outcast (2002), Jedi Knight: Jedi Academy (2003) (great Star Wars feeling, best light sabre duels ever, and force powers felt powerful)
* No One Lives Forever 2: A Spy in H.A.R.M.'s Way (2002) (excellent shooter, great writing, great stealth)
* Portal (2007) (short and sweet, and while it suffers the coordination / execution problem typical to 3d puzzlers, it's not too bad, and the excellent writing makes up for it)
* Republic Commando (2005) (a very atypical Star Wars game, showing a much more grounded view of the universe, and a great squad-based shooter)
* Splinter Cell (2002) (awesome stealth, together with the Thief series the pinnacle of the genre, great modern thriller story, great voice-acting)
* Unity of Command (2012) (extremely accessible light wargame, such an elegant and tight design, and challenging scenarios)
... a running theme is freedom of choice - to me, that's part of the point of playing a video game instead of reading a book or watching a movie - the ability to shape and influence what is happening, and choose what actions I take and how I affect the storyline.