Damn, what a stacked year 1998 was! For me, it's between Half-Life and Baldur's Gate, hard to decide. So many games that year that had such impact on entire genres, Starcraft, HL, BG, Thief: The Dark Project, F-zero X, Rogue Squadron, Fallout 2 etc. Crazy stuff.
I think I'm going to vote Baldur's Gate though, it's the closest to my heart genre-wise and gameplay-wise. Thief and MGS did wonders for the stealth genre (one could claim that Thief more or less invented it in its sheer form). But today, CRPGs are still my favorite genre, and they're having something of a renaissance of late.
Another thing that strikes me looking at that insane list is that it contains two former giants who have since destroyed themselves (Bioware, Blizzard), one that no longer produces games at a significant rate (Valve), two that were killed by time (Black Isle and Looking Glass) etc. It's as amazing as it is sad seeing what they did in the past. Just about the only developer among all of them who do anything worthwhile today is Nintendo.