The first 15 minutes of Bioshock were set so well that I thought I'd love the game. Then reality sunk in and it lost it's charm. If I could fix it, I'd make Big Daddies almost not fightable, ammo super rare, money found in super small increments and the plasmids and wrench the main combat choices. Oh, and while vita chambers are nice, punishing us for them would have made it more tense
My fav. part was when you heard screaming of splicers as you stood in the only lit area, I fired my shotgun all around me freaking out, then the lights came on and I saw all the bodies and though Holy Shit that was fucking awesome!
Also, Metroid Prime, the first one most of all. The Ridley fight and the dodging during it had me freaking out and moving my chair as I dodged attacks...it's one of those immersion settings that had you feel as frantic as Samus was, don't know if that counts as atmosphere but whatever, I was frantic and I'm sure Ms. Aran would be too if she had a voice (her Other M voice is a cross between Little Neil during Rocky Horror and a 20 year old college student who parties and drinks and sucks cock for "fun"...not the battle hardened 30-40 year old who sounded like the Samus I know and love)