Akira is always a good start, an excelent anime sci-fi movie, directed by Katsuhiro Otomo, who spent 10 years writing the manga it was based on (the manga is better btw, but the movie is still very good.)
Jin-Roh: The Wolf Brigade is a sci-fi movie, complex and thoughtful, and overall just well done.
Mushishi this may or may not meet your tastes, but I've liked a lot of the animes you mentioned, and I absolutely loved Mushishi. All episodes are standalone episodes, so the plot never gets too complex, but they are all deep and thoughtful, as well as beautifully animated. They tell the story of a traveling doctor who goes around a fantasy country treating people who are plagued by Mushi (think supernatural germs, although that is a gross oversimplification of the premise).
Fooly Cooly/FLCL/Furi Kuri are all different names for the same 6 episode long OVA series. The plot is definately intricate, it's quite funny all the way too, and to oversimplify this plot too it is a coming of age story, exploring the relationships the main character has with his family, friends, etc...