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These titles are not inherently Shonen/Seinen OR Shoujo/Emotional and have either a little of everything or something completely different or just don't fit into the normal genres. A lot of these titles, in my experience, are the best anime you'll ever see and thus "masterpieces" fits here.

Recommended Masterpieces/Misc Rating Comment
Allison & Lillia (TV) Excellent Absolutely beautiful series with a wonderful story spanning two generations of mother/daughter which focuses on romantic relationships in a living, breathing, and moving world and society.
Aquarion (TV) Excellent Very pleasing anime with good, well-fleshed out and loveable characters and romantic interest but very interestingly intertwined with the underlying idea of fate. Overall this show has a lot of value to it and is one of my top recommended mecha.
Bamboo Blade (TV) Excellent
Banner of the Stars (TV) Masterpiece
Banner of the Stars II (TV) Masterpiece
Banner of the Stars III (OAV) Masterpiece
(The) Beast Player Erin (TV) Masterpiece
BECK: Mongolian Chop Squad (TV) Masterpiece This anime has soul. It has a life of its own which would inspire anyone. Good fleshed-out characters, gripping storyline, and an amazing style that blows all preconceptions about anime out of the water. No one can regret watching this anime.
Blue Gender (TV) Excellent Reminiscent of 60's scifi bug-blasting but definitely should not be knocked. The characters may start off annoying but they grow and evolve and begin to really grow on you until you really can't help but wish for the same things as they, stupid as they may be. Good storyline, awesome and interesting music especially, and towards the end, very cute and sweet. Recommended for anyone serious about anime and wanting a good solid hard-hitting story.
Cardcaptor Sakura (TV) Excellent
Chiko, Heiress of the Phantom Thief (TV) Masterpiece
Claymore (TV) Excellent
Crest of the Stars (TV) Masterpiece
DNA² (OAV) Excellent
Eden of the East (TV) Very good
Fantastic Children (TV) Excellent
FLCL (OAV) Excellent
Freedom (OAV) Masterpiece
Fullmetal Alchemist: Brotherhood (TV) Masterpiece
Gin-iro no Olynssis (TV) Very good
(The) Girl Who Leapt Through Time (movie) Masterpiece
Haibane Renmei (TV) Excellent
Heroic Age (TV) Excellent
Infinite Ryvius (TV) Very good
(The) Irresponsible Captain Tylor (TV) Masterpiece
Jyu-Oh-Sei (TV) Excellent
Kaleido Star (TV) Excellent
Kimagure Orange Road (TV) Excellent
Kino's Journey (TV) Excellent
Kurau: Phantom Memory (TV) Very good
Kurenai (TV) Very good
Kurokami The Animation (TV) Excellent
Kyo kara Maoh! (TV) Excellent
Library War (TV) Excellent
Macross Frontier (TV) Excellent
Mobile Suit Gundam 00 (TV) Good
Mobile Suit Gundam 00 Second Season (TV) Very good
Mushi-Shi (TV) Excellent
Planetes (TV) Masterpiece Best-balanced romance anime there is that doesn't make light of relationships but at the same time isn't oppressingly mature and retains its cuteness. The male and female lead in this anime are two very loveable characters that balance each other well, as well as balancing the shonen and shoujo aspects of this anime. Their relationship is the cutest I've ever seen in anime. On top of that, the concept and world of this anime is both realistic and imaginative. This is one of my most favorite anime series.
Pom Poko (movie) Excellent
Shangri-La (TV) Very good
She, The Ultimate Weapon (TV) Very good
Sky Girls (TV) Excellent
Solty Rei (TV) Very good
Spice and Wolf (TV) Excellent
Stellvia (TV) Excellent
Strain: Strategic Armored Infantry (TV) Excellent
Tactical Roar (TV) Excellent A pseudo-harem anime which does better than most. I found this series to be cute, fun, with awesome theming and basic concept. This series is underrated and underwatched and while not inherently amazing, I recommend it for those veteran anime fans looking for something they haven't seen before but is still a good watch.
Tide-Line Blue (TV) Excellent A very compelling shonen series that deals with serious world affairs, serious relationships, and mature issues while still maintaining the positive and upbeat essence of shonen. It is a very solid series and everyone should see it.
(The) Twelve Kingdoms (TV) Masterpiece An amazingly compelling plot, especially later on in the series. Interesting characters who can be annoying and pathetic, yet seem human and though they can be delusional, you can feel their pain. But this is as epic as any shonen title, and more impacting for the serious plot and picture it presents as a portrayal of the good and bad of humanity, focusing just as much on the protagonist as it does on government officials, kings and queens and how they are people as well and subject to flaw. But, rulers of a kingdom can be damn cool. Overall I recommend this to anyone who likes a mature, well-developed story, political intrigue, and shonen. While it may not be shonen, it leaves you with much of the same feeling.