The form doesn't allow as much depth, in the sense that even a 52-episode series can only cover a short novel. But I've found some very thought-provoking works (as, to be fair, I have in comics); particularly:
I could name plenty more shows that were thought-provoking stories (Psycho-Pass and Eden of the East come immediately to mind), but these are the ones where the animated form seemed to really matter. (Though to be honest I'm surprised you list Death Note - I wouldn't call it especially thought-provoking, and it was a manga before it was an anime).
viewer-hostile
Wow, you're still sore over Endless Eight? I thought it one of the finer pieces of trolling ever indulged in by a commercial product. :)
This is the monthly thread for posting media of various types that you've found that you enjoy. Post what you're reading, listening to, watching, and your opinion of it. Post recommendations to blogs. Post whatever media you feel like discussing! To see previous recommendations, check out the older threads.
Rules: