Ergo proxy has had a big impact on me and basically got me out of shounen and into more seinen and mature stuff.
Space brothers hit me hard because of how much I could relate to the MC and how he hated his lifestyle, then being revitalized by picking up the passion he had as a child.
NHK ofc, has a very strong message while portraying the depressing lives many people lead today. The helplessness and depression mixed with dark comedy made me rethink what I did in life and strive for my goals.
Colorful, even though a bit cliche, is also important to me in how people cope with their reality, and change/adapt to it.
Shinsekai yori plays with humanitary and moral questions. I find it odd as to how people don't seem to finish it. Squealer best antagonist.
At this point I'm not sure how deep the disappearence is by definition, but it definitely hits home for me personally.
Steins gate may not be as deep as I find it fun and experimentive with time travel and alternate universes. It has some clever ideas though
Paprika is pretty cool
I only read monster manga but I found it quite clever too.
Bebop gets me emotional and is relatively deep at times.
Probably more but can't think of em atm/ at work lel