MGS2 for me. It was the first time a game actually made me sit back and reflect. I love how the game played with emotions like doubt and uncertainty and the definition of perception. No other game have done that since(to be honest it's quite rare in fiction in general). The way the game breaks down its own narrative through both gameplay and story into a self-referential parody of videogames and player agency makes this a genuine piece of, may I say it, post-modern
art. The game was also way ahead of it's time in regard to it's critique on information control and social and genetic selection. The themes of MGS2 run deep but are handled with such a meticulous care that a lot of the game is nigh on prophetic like 13 years later(social media, PRISM, information manipulation etc). The themes also loop back into the gameplay itself re-enforcing them as an interactive novelty that make you, the player, part of the experience rather than just the observant. MGS2 was essentially a satirical retelling of MGS1 deconstructed into philosophical soul-searching.
To think the same company that greenlighted MGS2 and the similarly avant-garde Silent Hill 2 now just want to make slot machines and cheap phone games; it just blows my mind(and not in a good way).
I enjoyed all the MGS games, but not really on a deeper, intellectual level like MGS2. To be honest I enjoyed the original Metal Gear games as well. I played the original on the MSX when I was just a few years old.

MGS1 was amazing when it came out and had a really good story, a slick spy-thriller(full of cutscenes *cough*) that defined a genre. MGS3 really broke out of the mold that MG1+2 and MGS1+2 started(break into fortress, defeat giant robot etc.) and was structurally very different from the previous games(including being bascially the start of the Big Boss origin story) but was still obviously absolutely superb.
Just to think we now arrived at Phantom Pain and seeing how games and technology have evolved in a little less than 30 years, and knowing that the same guy is still responsible, is nothing less than amazing. Not even the douchebag Konami exec can spoil that.
''You exercise your right to "freedom" and this is the result.
All rhetoric to avoid conflict and protect each other from hurt.
The untested truths spun by different interests continue to churn and accumulate
in the sandbox of political correctness and value systems.''