Let's see here. Some of these are repeats, some are new, and some are here for new reasons.
Wolfenstein 3d - Proving that it is possible to have a 3d based game engine up and running on a PC system.
Half-Life(2)/Neverwinter Nights - They're lumped together for one reason, and one reason only. They have a HUGE and still active modding community, in some cases making work as good as, if not better, than the original created material.
Battle.net - Yes, I know it's not a game. But you can't deny the influence on this very important system. It is the precursor of most, if not all gaming networks. If you want to include something important for everything afterwords, like say LIVE or PSN, then you look to battle.net.
Guitar Hero - This game proved that it's possible to take a hard plastic guitar, cover a bunch of songs(I still want to punch the guy that covered infected), and make a fun game that has spawned a bunch of sequels.
Goldeneye - 2 Reasons. First is that Movie Licenses don't have to suck as games. The second is that it is possible to put a fun, relatively fast paced FPS on a console with an analog stick.
Shadowrun(360/PC) - Yes, we all know the game sucks, and has killed a company, but it did prove one thing and one thing only. It is possible to get a 360 to talk to a PC and play the same game at the same time.