Really, anything involving Tsutomu Nihei, even the Sidonia 3dcg anime.
Shoujo Shuumatsu Ryokou's also got some neat, pretty Nihei-inspired megastructure architecture.
Finally, Texhnolyze does a lot of fun stuff with using architecture (in both Lux and the surface world) to contribute to atmosphere and tone as well as plot.
[0] https://en.wikipedia.org/wiki/Les_Cit%C3%A9s_obscures