For me it's a toss-up between Ruins and the tower itself. It's cliche now, but I'm a sucker for post-apocalyptic settings, especially when there are abandoned subways. I love subways :) (That part in Secret of Mana where you ride the subway makes my inner-child fist pump every time.)
The tower itself is awesome for the sheer variance and weirdness of the scenarios you encounter. Those people condemned to wallowing in that black swamp w/ gargoyles? The two mini-worlds connected by that drain? That one place where everyone is super busy -- what the hell could they be busy doing?! So creepy and awesome :)
I think he's talking about the same place I was talking about above, the place where everyone is super busy. I think it's laid out as two vertical conveyors/escalators in a small room.
Oh yeah, that's right. They were super busy with ... something.
But the Library was in the 4th World (Apocalypse) and only in the fan-translated games. (The US release had the clues "Ashura.. is... controlled... by...")
As for the fallout shelter, what made is sad was that these weren't just people who climbed the tower before you (corpses of them no less), but these were just kids who died of starvation and their big sibling sacrificed themselves by dying first and all alone in the basement clutching a nuke bomb.
Fighter: "Mr Pibb", "Dr Pepper".. I'm onto you.. Kaz Fact: Welcome to Version 2.0!