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There are many ways that can increase atmosphere in an MMORPG, and they're often not the same for everyone. Since we're all slightly different wired, and what does it for one person can leave another person completely indifferent and unaffected.
The beta gameplay I did of GW2 and TSW recently made me think of it.
TSW isn't exactly a horror game - a good example of a pure horror game would be Amnesia or Silent Hill - but it does have this lingering suspense and sense of foreboding at least to me that permeates the atmosphere in the areas you wander around in. It was in TSW that I noticed how quests when designed right can really add to that mood and vibe of an area. When I followed the mesmerising Siren Song, or tried to solve a serial killing that happened in Kingsmouth years ago by uncovering clues (definitely not a walk in the park as most quests in other MMO's), even on purpose died in order to search for the next clues in ghost form, these quests managed to gradually strengthen the otherworldly detached, suspenseful atmosphere that I felt the town gave off. It surprised me that the quests helped to do it, but I liked it.
Sort of the same but in a wholly different way was in GW2: how the human capital was built, the reactions of NPC's, even the DE's in Queensdale, altogether they managed to give me the vibe that GW's pre-Searing area gave off.
On reflection, I had the same in some other MMO's, when the designers have managed to do something just exactly right to deliver - to me - a strong, dominant atmosphere in an area: I had it when I wandered around in AoC in the Cimmerian region in the snowy mountains, when the music grew louder - some of the best ingame music I've heard - it really felt like Conan's Hyboria. And the same with when I first approached the cities of Stormwind and Ironforge or wandered through Teldrassil, with the great background music it really felt magnificent.
It doesn't happen often that an atmosphere feels just right and impressive, that's why those moments stick to memory. I'm glad that the new upcoming MMO's manage to deliver with it too.
But everyone is wired slightly different, this is what did it for me. What were moments in your MMO gaming life that you recall that the atmosphere really hit right for you? And did questing ever gave you that vibe? And did you feel it too with the new MMO's, that the atmosphere really got to you equaling memorable times in MMO's of your past?