Wolfenstein should not be on the list. It may have started the FPS genre but it wasn't really a household name. Doom being on the list, and being the more "defining" game, already covers Wolfenstein's influence by proxy.
Now, I absolutely agree on the other titles in the list. They definitely helped define what PC gaming was in the 90s. And though some might not have as far-reaching an influence as others (Myst) their collective impact on the industry and the gaming community during that time period can not be understated.
As to what could fill Wolfenstein's slot, I offer these examples:
Diablo: This game set a standard for almost every game of it's type. As well, it became an almost cultural phenomenon. It was rare to attend a LAN party or similar gathering and not see people playing this or simply talking about it. Doubly so for it's sequel.
Half-Life: Wolfenstein may have started the genre, and Doom may have cemented the genre as a staple, Half-Life defined what the genre could be and what potential there was in expanding on the old ideas. And not just in terms of story, level design, or game-play. It was one of the "watershed moments" in PC gaming during the 90s.
Quake 3 Arena: It wasn't the first online multiplayer FPS in the 90s. In fact, it came out near the end of the decade. However, it was, in a lot of ways, the prime example, the end result if you will, of the inception and progression of the concept of multiplayer, FPS online gaming. It was also incredibly influential within the professional gaming culture.
Unreal Tournament: Just about everything that can be argued for Quake 3 can be repeated here.
Ultima Online: Effectively brought the concept of large-scale, large player-count, online RPG gaming to the public space. MMOs had existed prior to this game but this was, in some ways, the Doom of the genre. Granted, like Quake 3 Arena, it came near the end of the decade. However, also like Quake 3, it was the ultimate example of the MMO concepts being borne out of the era.