If something is important in that sense, that usually means it is good though, right?
People still talk Doom because while HL and so forth may have refined the gameplay, they still aren't appreciably different. They certainly do look better, no doubt, but graphics are really of no consequence in this sense because newer games will always look better due to the advancing technology. The physics implementations that are possible now are also cool, but that is still a refinement of the core gameplay.
It means it was good, not that it still is. A newer game that refines the gameplay still improves upon the game and is inherently a better game for that improvement. This, plus newer features, constitutes an appreciable difference. Scripted events, friendly AI, puzzles, are all things not even included in Doom that help make Half-Life "appreciably" different and a better game than Doom is. And this is beside the fact that what you are trying to attribute to Doom actually belongs to Wolfenstein 3D and the main reason people mentioned Doom instead of Wolfenstein 3D is that Doom is considered a better game.