Awesome Music: The opening theme, "Duvet" by boa, as well as the long psychedelic jam that plays over the Info Dump in "Infornography".
Big-Lipped Alligator Moment: Given the show's Mind Screw nature, there's a ton of these, though some do get Call Backs, which prevent them being "true" BLAMs. However, there are several completely inexplicable scenes that happen throughout the show, including:
The scene in which ectoplasm starts emanating from Lain's fingers in Layer 01.
The train suicide in Layer 01.
Pretty much all the scenes involving PHANTOMa in Layer 04.
The alien in Lain's doorway in Layer 09.
The Men in Black suddenly dying horribly, which is never even referred to again.
Ear Worm: The theme song, "Duvet" by boa, is catchy as hell.
"Funny Aneurysm" Moment: Certain ideas about the users of the Wired are eerily similar to the users of a very popular real-life imageboard.
Genius Bonus: As mentioned on the main page, the series gets easier to understand if you're familiar with some of the more esoteric concepts it talks about.
Les Yay: The only two people Lain ever has any real connection to are Alice and, to a much lesser extent, Mika. Alice and Lain, however, are not related and occasionally have... shall we say, moments of intimacy that go far beyond mere friendship. Hell, Lain even tells Alice she loves her towards the end, though the circumstances imply it's agape, not eros.
Moe: Lain has a number of the physical characteristics and early on is often presented in a "cute" way (with her bear outfit or hanging out in just her nightgown). She absolutely does not have a matching personality, though, and as the series goes on it feels far more like a Deconstruction or even an attack on the trope.
"Protocol 7 is expected to allow the seamless sharing of information, information that will be shared between the Wired and the real world. And now, the following message. Let's all love Lain. [Slasher Smile] Let's all love Lain, let's all love Lain, let's all love Lain, LainLainLainLainLainLainLainLainL-l-l-l-l-l!"