So so very hard to pick even just a handful. But I'll have a go...
In no particular order:
Diablo II: Just the best implementation of the isometric action RPG style. Awesome story and atmosphere, and addictive loot system. Countless upon countless hours spent in that game! Baldur's Gate and Nox are close as far as isometric RPGs are concerned.
Thief Gold: Needs no introduction in these circles. A genre-defining game that didn't reach the popularity it deserved. The aesthetic and story are to me what put it above games like Thief II and Deus Ex, though they are close.
S.T.A.L.K.E.R: Shadow of Chernobyl: Absolutely mind-blowing game in so many ways, despite the bugs. Aesthetic, story, mood/environment, factions, enemies, inventory system and so much else were just perfect in this game.
Total Annihilation: This is to me the pinnacle of the RTS genre. The first game to my knowledge that had units that didn't need constant micro-management, and a truly well implemented elevation system. Besides, the "game universe" was just too cool! Close runners up are StarCraft and C&C: Red Alert.
Star Wars Knights of the Old Republic: Just a complete gamechanger for immersive 3D RPGs. The depth of the lore, detailed environments and tie-ins with the movies made this an instant classic imo. It represents the very best of Bioware. I suppose games like The Elder Scrolls fall in to this category too, even though in my mind they are apples and oranges. Oblivion stands out to me as equally great as SWKotOR.
To bring this post out of it's nostalgic trance I can also mention some more modern games that I've almost wanted to put on this list, most of which I've poured hundreds of hours into.
TDM? I think that counts ^^
Escape from Tarkov (Online survival shooter ála Stalker)
Star Wars: The Old Republic (MMO-RPG)
Dirt Rally (Rally/racing simulator)
Overwatch (Online FPS with MOBA elements)
Divinity: Original Sin 2 ("faux-isometric" turned based RPG)