These Three are imo, the best out of all. They don't throw overused tropes at you, are all incredibly thought provoking, and are definately "Masterpieces".

1 - Legend of Galactic Heroes - http://myanimelist.net/anime/820/Ginga_Eiyuu_Densetsu This series, literally there are no words to describe it. I don't enjoy the old art style, and the first few episodes were a struggle. But once you've started it properly, you just don't stop. It plays on political science themes, and excellent character development, as the two main characters struggle against each other, with difference ideologies - a Benign authoritarian state versus a corrupt democracy. I won't say anymore, as they would probably be spoilers. But the series is phenomenal, and I really recommend it no matter what your favourite genre is.

Two - Monster - http://myanimelist.net/anime/19/Monster Again another series that causes us to ask questions. I despise murder mysteries normally, but this one is an exception. Whilst I don't feel it is as deep as number one, its still a good series. Been a long time since I watched it though, so I can't sum it up easily.

3 - Beserk - http://myanimelist.net/anime/33/Berserk This shit is griiim, I don't like Manga, but with beserk I just had to find out what happened. Literally one of the most brutal and well written stories I've ever seen. The character development of Guts is amazing, and the cruelty the author inflicts on him and other characters makes me adore the series even more. Imagine if George RR Martin suddenly decided to add more fantasy elements, and step the brutality up a notch, and you'd find beserk sitting there, drunk on blood, wine and piss. Both the Film or Anime are good, and are really up to personal preference which ones you watch first as they both cover the same point in time.