It's hard to pick just one:
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Deus Ex. It's timelessly topical despite being released in 2000. It predicted the War on Terror and a massive pandemic to name a couple.
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Spiritfarer, for maximum onion chopping. Saying goodbye to Gwen really messed me up since I became very attached to her, and I can't finish the last stretch of the game because it's too emotionally taxing.
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Undertale and wholesome fan-games like Act to Flirt.
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Half-Life 2, circa 2004 when it was a leap ahead of everything else. I was unsettled by the teaser screenshots due to how real it all seemed to be during its heyday. (I did re-capture part of that feeling with M Mod and its great yet faithful modernisation effects. Plus there's some blursed mods you can combine with it such as replacing Alyx with Krystal, voiced by the original actress.)
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Duke Nukem 3D: Alien Armageddon. It blew me away how much custom content and passion has been invested, so good that it almost felt like I was playing Duke Nukem for the first time all over again.
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There's many more worth mentioning such as Unreal, Morrowind, Oblivion, Company of Heroes 1 and the forgotten gem that is Ground Control.
Man, I was born just at the right time to experience a stunning variety of titles and enjoy the mods that improve them.