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Seen all Rating Comment
5 Centimeters Per Second (movie) Excellent The only reason I cant rate this a "Masterpiece" is because, in the end, it is quite depressing. Despite being something of a romance, I think it appeals to both sexes about equally. It starts out with the tone of a happy childhood dream (Whisper of the Heart~esque) but as the characters age the harsh realities of life are discovered instead.

This anime is more about "what could have been" than it is about what actually happened.
Akira (movie) Masterpiece
Angel Beats! (TV) Excellent
Appleseed: Ex Machina (movie) Decent This movie is about a kind of political power struggle in the last remaining heaven for humanity. There are mechas, which are kind of cool, but the movie itself isn't about mechas.
Berserk (TV 1997) Very good
Blood+ (TV) Masterpiece
(The) Cat Returns (movie) Decent If you enjoyed Whisper of the Heart, you should enjoy this one as well. I don't think I'd recommend it independently of that anime but if you're a fan of other Studio Ghibli films you'd probably enjoy this one as well.
Denpa teki na Kanojo (OAV) Excellent
Elfen Lied (TV) Excellent Complete with naked chicks tearing off the heads of security guards, this anime has a pretty good story and is worth watching.
Ghost in the Shell (movie) Excellent
Kanon (TV 2/2006) Good
Kurokami The Animation (TV) Very good The story for this anime is actually really good but the synchro "power up" scenes are kind of cliché.

The manga is supposedly really good so maybe it just didn't scale up as an anime as well as it could have.
Lucky Star (TV) Masterpiece
Magical Shopping Arcade Abenobashi (TV) Very good
My Neighbor Totoro (movie) Excellent
Noein - to your other self (TV) Masterpiece
Perfect Blue (movie)
Rurouni Kenshin: Reflection (OAV) Very good
Rurouni Kenshin: Trust & Betrayal (OAV) Very good
Samurai 7 (TV) Decent
Spirited Away (movie) Masterpiece
Tokko (TV) Good This anime ended a bit abruptly. It's pretty good but I think it deserved more episodes.
Welcome to the NHK (TV)
When They Cry - Higurashi (TV) Masterpiece If you're looking for an anime with a lot of mystery, this is probably one of the best. Although it's often classified as a "murder mystery", it really has nothing to do with detective work. The anime is full of clues but most of the correct ones are very subtle. It also waits till the very end to begin explaining parts of the story. The main mystery, which is only really revealed close to the end of this anime, is explained in the squeal "ni kai".

Even though the main mysteries are explained in this anime and the squeal, there are plenty other mysteries in the various story arcs which are never explicitly explained, although a bit of digging on the Internet (or maybe a smart wit) reveals that enough information is given to explain all the particulars of the various story arcs.
When They Cry - Kai (TV) Masterpiece Squeal to the first "When they Cry" anime. This is where most of the story is explained so it is definitely a must see if you plan on watching the first one.
When They Cry - Rei (OAV) Decent This is a short story arc complete with all the characters from the previous "When they Cry" animes. It takes place after the last arc in ni kai but it doesn't really add to the main story.
Whisper of the Heart (movie) Very good
Wild Arms - Twilight Venom (TV) Very good
Witch Hunter Robin (TV) Good