I highly recommend sousou no frieren. The way it builds its magic system and world is incredibly creative, and it's exactly the kind of magical world I've always imagined.
I recommend Shinsekai yori (From the New World): Starts like a peaceful rural mystery with psychic kids, then spirals into a dark, brilliant look at morality and social control. The final arc is phenomenal.
For me, it's definitely A Silent Voice (Koe no Katachi). The emotional journey and the redemption arc really hit hard. Another one would be Oyasumi Punpun—it left me feeling completely drained and melancholic for days.