Not a desert island list, as that would be defined by replay value. It is a personal top-tenhundred, and some games are above their proper rank for personal nostalgic reasons. Add-ons are generally included, unless specified otherwise. For online games, I specified the period with which I associate them.
1. Victoria II - the perfect game for creating grand historical narratives. Less focused on 'winning' and map-painting than other Paradox games, has a lot more non-combat content. Makes you read the history of the state you chose, including the parties, major movements, cultural regions, etc. The setting is perfect. Great replayability. There are many hidden mechanisms that are altered in mods, so it is hard to game the system too much. Watching what the AI does with the rest of the world is a significant component of the story. Now playing Czechoslovakia in the 1910s, with Prague being somewhat bigger and more industrialised than London thanks to an early focus on social welfare, pop growth techs, and the preemptive expansion of factories (I am getting so many workers that I cannot change the industrial profile of Bohemia). Probably the most memorable episodes were preserving apartheid with South Africa in NWO, forging Korea into an industrial giant without an implausible colonial empire, and restoring an economically advanced Greece through diplomacy. The combat interface is too cumbersome and time-consuming, and war is too easy to exploit towards the end, so I prefer realistic peaceful strategies.
2. Heroes of Might and Magic III - elegant gameplay, excellent replayability, good map-making and modding community. Seems like the only exceptional strategy on mobile platforms, too.
3. Baldur's Gate I (sans add-on) - mostly for very strong nostalgic reasons, but also for its superior and free-form exploration element, compared to relatively streamlined and plot-driven IE games. I like its unusual focus on low-level adventuring, since most serious fantasy games quickly spiral out of control into dragons, demons, and summoning meteors. I also enjoy the uncommonly large selection of companions, though they are not elaborate enough. Sadly, not too fun to replay.
4. Gothic II: Night of the Raven - uniquely well-designed exploration. Good character progression and atmosphere, though the plot and writing are a bit subpar, even if the conceptual approach to dialogues is good - no walking encyclopaedias here.
5. Civilization IV - chiefly because of its highly sophisticated and competitive multiplayer (see RealmsBeyond for a sample), but also for the grand narrative it makes you create in your mind. I especially enjoy the geographical element - e.g., you might happen to be a thalassocratic empire with scarce natural resources, but a good position for diplomacy. Initial exploration is sweet (Thea capitalises on that aspect of Civ). The game is quite well-balanced and lends itself well to theorising. Decent difficulty in single-player.
6. Vampire: The Masquerade - Bloodlines - better than any major RPG except P:T when it comes to dialogues. Memorable interactive characters. Good implementation of a setting I enjoy (I read WoD rulebooks for pleasure).
7. Age of Wonders: Shadow Magic - impressive diversity of units and races, overland and economic magic. Has some excellent player-made grand scenarios (e.g., Gates of Elocin). Really pretty, even more so than the map in HoMM3. The AI is a bit flawed, alas, so pre-made scenarios are the best choice.
8. Eador: Genesis - tough gameplay and interesting development of units, especially with New Horizons. Has the same appeal as AoW:SM. Great for playing while listening to an audiobook. The campaign is lousy; I only play random maps.
9. Ultima Online [~2001] - the perfect sandbox MMO with so many things done right. No "levels", no instances, no zones intended for this or that level, proper housing, punishing death, full loot, much less emphasis on equipment than is common now, good exploration, no silly "quests", emphasis on player-created content, etc. Generally, a lot of freedom, including opportunities for exploitation. Importantly, it is no mere nostalgia. The gameplay still holds up on independent servers, though the public is a bit trashy and too scarce.
10. King of Dragon Pass - an intricate story system with good writing and plenty of elaboration on the setting. Loved the mythology and the counter-intuitive customs. Gradually falls apart after a few replays, but highly atmospheric and alive initially.
11. Sid Meier's Alpha Centauri
12. Space Rangers II
13. Gothic I
14. Underrail
15. Crusader Kings II
16. Victoria I (Victoria II is strictly better, however)
17. Mount & Blade
18. ADOM
19. Unreal Tournament
20. Age of Wonders I
21. Geneforge IV
22. Hearts of Iron II
23. Jagged Alliance II
24. Cybernations [~2007]
25. X-Com (Long War mod)
26. SW: KOTOR I
27. SW: KOTOR II
28. Anachronox
29. Might and Magic VI
30. Battle Brothers
31. Magic: The Gathering (1997)
32. Warlords II
33. Rome: Total War
34. Revenant
35. Sam & Max Hit the Road
36. Arx Fatalis
37. Wizardry VIII
38. Faster than Light
39. Warhammer 40k: Dawn of War I
40. Neverwinter Nights I (add-ons and mods)
41. Master of Magic
42. Hearthstone [~2015]
43. Civilization III
44. Europa Universalis III
45. Geneforge V
46. Risen (may go up, but a bit too derivative of Gothic II and has a really irritating obligatory quest)
47. Avernum V
48. Civilization I
49. Disciples II
50. Star Wars: Jedi Knight II (multiplayer)
51. Lords of Waterdeep (tablet)
52. Temple of Elemental Evil
53. Warchaos [~2009]
54. King's Bounty (2008, haven't played the add-ons)
55. Thea: The Awakening
56. Indigo Prophecy (Fahrenheit)
57. Might and Magic VII
58. Elder Scrolls Online [~2014]
59. Princess Maker II
60. Icewind Dale I
61. Chronicles of Riddick: Escape from Butcher's Bay
62. Evil Islands
63. Woodruff and the Schnibble of Azimuth
64. Gorky 17 (Odium)
65. Nox
66. Age of Empires I
67. Ultima VII: The Black Gate
68. Rollcage
69. World of Warcraft [~2005]
70. Dungeons and Dragons Online [~2009]
71. SW: TOR [~2012]
72. Alone in the Dark I
73. Caves of Qud
74. Heroes of Might and Magic II
75. Icewind Dale II
76. Path of Exile [~2013]
77. Xenonauts
78. Knights of the Chalice
79. World of Tanks [~2010]
80. Master of Orion II
81. Divinity II
82. South Park: The Stick of Truth
83. Blade Runner
84. Diablo II
85. Twilight Struggle (tablet)
86. Clash Royale (tablet)
87. TESV: Skyrim
88. TESIII: Morrowind
89. MechCommander
90. Darkest Dungeon (sped up)
91. Grim Dawn [~2017]
92. The Witcher
93. Blades of Steel (NES)
94. Tecmo Basketball (NES)
95. Majesty: The Fantasy Kingdom Sim
96. IndyCar Racing
97. Tony Hawk ProSkater III
98. Heroes of Might and Magic IV
99. Descent
100. Zanzarah
I haven't properly played a bunch of popular games like Age of Decadence, New Vegas, MotB, or Expeditions: Conquistador, since they don't seem to work well on my PC, which I refuse to upgrade. I started Deus Ex and Thief at some point, but got distracted from them by life events, so I'll get back to them some time later on.
Baldur's Gate 2 (sans the add-on) and Planescape: Torment would be around position 3, Arcanum around position 15, Fallout I around position 20, and Fallout II around position 25.