How about Planescape Torment? I never played it myself but I have many friends that rave about the variety and intricacy in that game, and nothing else seems to have recaptured that.
One of the more philosophical games ever made.
Along those lines, a game that marked in many ways the high-water mark and end of what is now an extinct genre - Grim Fandango. At one time "Adventure Games" were a major share of the market. After Grim Fandango, major studios ceased to make Adventure Games as they seemed to feel that the market wasn't big enough to justify the expense. Adventure Games began to incorporate action/shooter and RPG elements, and action/shooter and RPG games began to do more with cut scenes and carefully plotted storylines. Now you have things like "The Last of Us" and "Uncharted" that have story going but aren't accessible or enjoyable to the gamers that purely enjoyed playing out the story without heavy reliance on combat, reflexes, and so forth.
Agree with those that saying Moo2 is still the high point of the 4X genre. I do think that Ascendancy could have gotten there, but the game was so buggy and the AI so bad. Stellaris is a spiritual successor to Moo2, but I just don't find it nearly as compelling.
I personally think Civ2 is the high point of the series, though I do agree that Civ4 is good, the game play in Civ4 feels more artificial to me (though not nearly as artificial as that of Stellaris). I'm also not big on the RPG elements that have crept into the game like faction units and faction buildings.
I'm personally OK with 1998 as the high mark in video games. Starcraft came out that year and with only a bit of updates, still conceptually dominates the RTS community. Grim Fandango is still high on almost everyone's 'greatest game of all time' list. Half-Life is a genre defining game that has rarely been surpassed. You have 'The Legend of Zelda: Ocarina of Time' that year. Balder's Gate came out that year. Unreal came out that year. Sports games like Madden and FIFA were getting close to entering their final form, with almost all evolution since then being more detailed textures. The original Gran Turismo came out that year.