One of the things that kept me engaged with Quake, aside from the obvious action, secrets discovery and visual engagement and atmosphere, was the huge number of mission packs and fan made levels ... I even made some myself, the only game I have bothered to do that with. And I even dabbled a lot with Quake Bots in the many MP levels.

Even so, like I said, I don't know which I prefer. Each type of FPS appeals to me for various reasons and have a lot to do with my mood at any one time.

And as I tried to indicate earlier, and as some have suggested, the lines are not that clearly defined much of the time. With Quake you have a story, even if a kind of loose one, but the atmosphere and sense of evil presence provide a great backdrop, which in a way is an evolving story. And part of the story, is also the alien and fantasy elements.

In some ways as has been said, Half-life is just a variant take on Quake, with a less fantastical setting. Quake 2 is even more alike.

As has been said before, I think discussions about different types of FPS are unlikely to really be about the game having a story or not, it's more about how the story is presented and how that interferes with the gameplay and pacing, e.g. whether there are a lot of cinematic cutscenes (which can be cool but take away time and action from the player), whether there is a lot of scripting (requiring the player to be patient, to slow down, wait, or do things in other very specific ways), whether the levels are open or linear corridors.

And it isn't always as clear cut, for example what about Hedon, which has retro graphics and plays like Doom but has a more elaborate story, huge open levels somewhat reminiscent of Arx Fatalis, alternative or secret paths through vents reminiscent of Deus Ex and Half-Life and even some light adventure game style puzzles, yet no real cutscenes or scripted events?

As far as preferences go, for me it really depends on the individual titles, not the subgenre. I'm on the same page with toxicTom though, I don't really like the third kind much, the arena shooters.

Story-based FPS don't result in as many playthroughs for me as the just-shoot-stuff games. Also, a good or interesting story is very subjective and thus dependent on the individual game. For example, I don't find BioShock appealing to any degree but thought Stalker was really cool.

The just-shoot-stuff games are typically always fun though for me, unless it's a rogue-like of sorts or has random levels.

I'm much more picky with story-based FPS than with Doom-style games.

I remember loving that as a kid, those 90's DOS cutscenes are still magic today. However I do think it's on a different level than Half-Life, which basically starts with a 30 minute interactive cutscene. You're right though, Dark Forces is a very early step toward more story focused shooters.

definitely story mode, if there ain't something like a good story around i won't play this genre ..so wolvenstein yay doom nay

Prefer not to choose one over the other. If the game is enjoyable, then I'll continue playing it. If it's really enjoyable, I'll play it again and again.