Thinking just in terms of influence, historical significance and longevity rather than subjective quality is pretty tough since we all have out favourites we'd like to see validated.
With that in mind I think Rogue should probably be in there. One of the great granddaddies of both procedurally generated levels and dungeon crawling in general. Plus of course the origin of the term "rogue-like" and "rogue-lite" which have become extremely common, particularly among indie games.
On a similar note, the games for which the "Metroidvania" trope is named probably deserve to at least be considered. Aside from their influence, they're both classic games in their own right. Same goes for the original Zelda.
Half-Life completely redefined the FPS genre and took immersive storytelling to a whole new level. It was also later modded into several games (most notably Counter-Strike & Team Fortress) that have themselves become classics in their own right.
Goldeneye might also be worthy just for it's influence on the multiplayer splitscreen side.
That's all I can think of for now.
Though I wonder how they're going to treat long-running series. Like the Legend of Zelda for example. Do you just take the series as a whole, or would they consider inducting multiple games from the same series (the original, Link to the Past, and Ocarina of Time probably being the top ones to consider)?
In the case of Zelda I'd say it should be the original as in terms of game mechanics, most Zelda games are basically the same and have just iterated on and refined what the original did. That said I can see a very strong and valid case for Ocarina being made.
