Serial Experiment Lain, Haibane Renmei, Elfin Lied, Serei No Moribito, Ghost in the Shell- the Laughing Man or Stand Alone Complex, for ones not previously listed. But I agree with FLCL, and Boogiepop Phantom, .
Close but am not so certain if it merits being in such vaunted company, Jin-Roh, the Wolf Brigage.
For me though Lain was maybe a bit too far over the top, especially as I really don't have a degree in computer science.
I could say the Melancholy of Haruhi Suzumiya, as it really stretched my mind just trying to keep up with what is what. I would have hated to try to watch the show as broadcast. I still have yet to do that.
I am close to saying Last Exile, but it kind of loses integrity in the last few episodes, and wraps up to quickly, as if they were not granted a third season or something, and really wanted to not leave things at a complete dead end. Dunno.
I'd say Kenichi History's Mightiest Disciple, simply for the way for some reason I just love that show to pieces. It isn't History's Greatest Anime or anything. It just gets me all excited. It would be like trying to explain why I like the color yellow. I just do, okay? lol
And from when I was not into anime, but liked to see animated movies, back when hardly anyone besides Disney was doing animation, Nausicaa of the Valley of Wind, Akira, Ghost in the Shell, Castle in the Sky. Ghibli films pretty much blow me away.