This list only includes anime I'd consider to be mostly sophisticated. In other words, anime with some type of story or purpose other than toilet humor or fanservice. These are the philosophical or psychological oriented programs or those that deal with moral issues or sensitive topics.

Anime (Sophisticated) Rating
Yukikaze (OAV) Excellent
xxxHOLiC: Shunmuki (OAV) Good
xxxHOLiC: Rō Adayume (OAV) Decent
xxxHOLiC: Rō (OAV) Good
xxxHOLiC: Kei (TV) Excellent
xxxHOLiC the Movie: A Midsummer Night's Dream Excellent
xxxHOLiC (TV) Very good
Xam'd: Lost Memories (ONA) Very good
Wolf's Rain (TV) Very good
Wolf's Rain (OAV) Weak
Wolf Children (movie) Very good
Witch Hunter Robin (TV) Excellent
White Album 2 (TV) Excellent
White Album (TV) Excellent
Whisper of the Heart (movie) Masterpiece
When They Cry - Higurashi (TV) Masterpiece
Welcome to the NHK (TV) Masterpiece
Votoms Finder (OAV) Very good
Voices of a Distant Star (OAV) Decent
(The) Vision of Escaflowne (TV) Masterpiece
Viper's Creed (TV) Good
Vexille - 2077 Isolation of Japan (movie) Good
Utawarerumono (TV) Excellent
Umineko - When They Cry (TV) Excellent
(The) Twelve Kingdoms (TV) Excellent
Tsukumo (movie) Excellent
True Tears (TV) Excellent
Toward the Terra (TV) Very good
Towanoquon (movie series) Excellent
Toshokan Sensō: Kakumei no Tsubasa (movie) Masterpiece
Tokyo Magnitude 8.0 (TV) Masterpiece
Tokyo ESP (TV) Very good
To (OAV) Excellent
Time of Eve (ONA) Masterpiece
Time of Eve (movie) Masterpiece
This Ugly Yet Beautiful World (TV) Excellent
(The) Third: The Girl with the Blue Eye (TV) Excellent
They Were 11 (movie) Excellent
Texhnolyze (TV) Decent
Super Dimensional Fortress Macross II: The Movie (OAV) Good
(The) Super Dimension Fortress Macross: Do You Remember Love? (movie) Masterpiece
(The) Super Dimension Fortress Macross (TV) Excellent
Summer Wars (movie) Masterpiece
Stratos 4 Advance Kanketsuhen (OAV) Excellent
Stratos 4 Advance (OAV) Excellent
Stratos 4 (TV) Excellent
Stratos 4 (OAV) Excellent
Strain: Strategic Armored Infantry (TV) Good
Stink Bomb (movie) Decent
Stellvia (TV) Good
Steins;Gate Fuka Ryōiki no Déjà vu (movie) Masterpiece
Steins;Gate (TV) Masterpiece
Starship Operators (TV) Excellent
Star Blazers 2199 (TV) Masterpiece
Spice and Wolf II (TV) Excellent
Spice and Wolf (TV) Excellent
Space Symphony Maetel ~Ginga Tetsudō 999 Gaiden~ (TV) Very good
Solty Rei (TV) Excellent
Sola (TV) Excellent
Sol Bianca: The Legacy (OAV) Excellent
Sol Bianca (OAV) Decent
Sōkō Kihei Votoms: Koei Futatabi (OAV) Very good
(The) Sky Crawlers (movie) Good
(The) Skull Man (TV) Good
Silent Möbius 2 (movie) Excellent
Silent Möbius (TV) Good
Silent Möbius (movie) Excellent
Short Peace (movie) Very good
Shiki (TV) Excellent
Serial Experiments Lain (TV) Excellent
Scrapped Princess (TV) Excellent
Samurai Champloo (TV) Excellent
Samurai 7 (TV) Excellent
Ryoko's Case File (TV) Excellent
Rurouni Kenshin: Trust & Betrayal (OAV) Excellent
Rurouni Kenshin: New Kyoto Arc (OAV) Good
Rumbling Hearts (TV) Masterpiece
(The) Rose of Versailles (TV) Very good
Robotics;Notes (TV) Very good
Rideback (TV) Masterpiece
Requiem from the Darkness (TV) Excellent
Red Garden (TV) Excellent
REC (TV) Masterpiece
Real Drive (TV) Masterpiece
Read or Die (OAV) Masterpiece
Ray (TV) Very good
RahXephon: Pluralitas Concentio (movie) Very good
RahXephon (TV) Excellent
R.O.D -The TV- Excellent
Pumpkin Scissors (TV) Good
Puella Magi Madoka Magica The Movie Part 3: Rebellion Excellent
Puella Magi Madoka Magica the Movie Part 2: Eternal Very good
Puella Magi Madoka Magica the Movie Part 1: Beginnings Very good
Puella Magi Madoka Magica (TV) Excellent
Psycho-Pass 2 (TV) Excellent
Psycho-Pass (TV) Excellent
Psychic Detective Yakumo (TV) Good
Princess Mononoke (movie) Masterpiece
(The) Princess and the Pilot (movie) Very good
(Le) Portrait de Petite Cossette (OAV) Excellent
Planetes (TV) Masterpiece
(The) Place Promised in Our Early Days (movie) Masterpiece
Phantom ~Requiem for the Phantom~ (TV) Good
Phantom - The Animation (OAV) Very good
Perfect Blue (movie) Masterpiece
Patlabor: The Movie Masterpiece
Patlabor WXIII (movie 3) Decent
Patlabor The Mobile Police: The New Files (OAV 2/1990) Very good
Patlabor the Mobile Police (TV) Excellent
Patlabor The Mobile Police (OAV 1/1988) Excellent
Patlabor 2: The Movie Excellent
Patema Inverted (movie) Excellent
Parasite Dolls (OAV) Excellent
Paranoia Agent (TV) Good
Paprika (movie) Masterpiece
Pale Cocoon (OAV) Masterpiece
Outlaw Star (TV) Excellent
Now and Then, Here and There (TV) So-so
Noir (TV) Excellent
Noein - to your other self (TV) Excellent
No. 6 (TV) Very good
Nisemonogatari (TV) Excellent
Niji-Iro Hotaru ~Eien no Natsu Yasumi~ (movie) Excellent
Nerawareta Gakuen (movie) Excellent
Nekomonogatari (Black) (TV) Excellent
Nausicaä of the Valley of the Wind (movie) Masterpiece
Natsuyuki Rendezvous (TV) Good
Natsu no Arashi! Akinai-chū (TV) Excellent
Natsu no Arashi! (TV) Excellent
(The) Mystic Archives of Dantalian (TV) Good
Myself; Yourself (TV) Masterpiece
Mushishi: The Next Chapter (TV) Very good
Mushishi Tokubetsu-hen: Hihamukage (special) Very good
Mushi-Shi (TV) Very good
Moribito - Guardian of the Spirit (TV) Masterpiece
Moonlight Mile 2nd Season - Touch Down (TV) Good
Moonlight Mile (TV) Good
Monster (TV) Masterpiece
Monogatari Series Second Season (TV) Excellent
Mobile Suit Zeta Gundam (TV) Excellent
Mobile Suit Victory Gundam (TV) Good
Mobile Suit Gundam: The 08th MS Team, Miller's Report (movie) Decent
Mobile Suit Gundam: The 08th MS Team (OAV) Excellent
Mobile Suit Gundam: Char's Counterattack (movie) Excellent
Mobile Suit Gundam Wing: Endless Waltz Special Edition (movie) Very good
Mobile Suit Gundam Wing: Endless Waltz (OAV) Excellent
Mobile Suit Gundam Wing (TV) Excellent
Mobile Suit Gundam UC (OAV) Masterpiece
Mobile Suit Gundam Seed Destiny Final Plus: The Chosen Future (OAV) Very good
Mobile Suit Gundam Seed Destiny (TV) Very good
Mobile Suit Gundam Seed C.E.73: Stargazer (ONA) Very good
Mobile Suit Gundam Seed (TV) Excellent
Mobile Suit Gundam MS IGLOO: Apocalypse 0079 (OAV) Very good
Mobile Suit Gundam MS IGLOO 2: Jūryoku Sensen (OAV) Very good
Mobile Suit Gundam F91 (movie) Very good
Mobile Suit Gundam 0083: Stardust Memory (OAV) Excellent
Mobile Suit Gundam 0080: War in the Pocket (OAV) Good
Mobile Suit Gundam 00 the Movie: A Wakening of the Trailblazer Very good
Mobile Suit Gundam 00 Second Season (TV) Very good
Mobile Suit Gundam 00 (TV) Excellent
Mobile Suit Gundam - The Movie Trilogy Excellent
Mobile Suit Gundam (TV) Very good
Metropolis (movie) Not really good
Mermaid's Scar (OAV) Excellent
Mermaid Forest (OAV) Very good
Mermaid Forest (TV) Excellent
Memories (movie) Decent
(The) Melancholy of Haruhi Suzumiya (TV) Very good
(The) Melancholy of Haruhi Suzumiya (TV 2009 renewal) Very good
Megazone 23 Part III (OAV) Good
Megazone 23 Part II (OAV) Excellent
Megazone 23 (OAV) Excellent
Master Keaton (TV) Excellent
Master Keaton (OAV) Excellent
Mardock Scramble: The Third Exhaust (movie) Very good
Mardock Scramble: The Second Combustion (movie) Very good
Mardock Scramble: The First Compression (movie) Excellent
MAOYU (TV) Excellent
Magnetic Rose (movie) Decent
Maetel Legend (OAV) Very good
Madlax (TV) Excellent
Macross Zero (OAV) Very good
Macross Plus Movie Edition Excellent
Macross Plus (OAV) Very good
Macross Frontier: Sayonara no Tsubasa (movie) Excellent
Macross Frontier: Itsuwari no Utahime (movie) Excellent
Macross Frontier (TV) Excellent
Lunar Legend Tsukihime (TV) Excellent
Loups=Garous - The Motion Picture Very good
Lost Chapter of the Stars - Birth (special) Excellent
Log Horizon (TV) Very good
Listen to Me, Girls. I Am Your Father! (TV) Excellent
Library War (TV) Excellent
A Letter to Momo (movie) Very good
(The) Legend of the Legendary Heroes (TV) Good
Legend of the Galactic Heroes: Spiral Labyrinth (OAV) Excellent
Legend of the Galactic Heroes: Overture to a New War (movie) Excellent
Legend of the Galactic Heroes: My Conquest is the Sea of Stars (movie) Excellent
Legend of the Galactic Heroes: Golden Wings (OAV) Excellent
Legend of the Galactic Heroes: A Hundred Billion Stars, A Hundred Billion Lights (OAV) Excellent
Legend of the Galactic Heroes (OAV) Masterpiece
(The) Legend of Black Heaven (TV) Excellent
(The) Laughing Target (OAV) Very good
Kurogane Communication (TV) Very good
Kurenai (TV) Masterpiece
Kurau: Phantom Memory (TV) Excellent
Koi Kaze (TV) Masterpiece
Kino's Travels: Life Goes On (movie) Very good
Kino's Journey (TV) Very good
Kino no Tabi: The Beautiful World (movie) Very good
King of Thorn (movie) Excellent
Kimi ni Todoke 2nd Season (TV) Excellent
Kimi ni Todoke - From Me to You (TV) Excellent
Kimi ga Nozomu Eien ~Next Season~ (OAV) Excellent
Kemonozume (TV) Masterpiece
Katanagatari (TV) Very good
Karas (OAV) Excellent
Kara no Kyoukai: Mirai Fukuin (movie) Excellent
Kanon (TV 2/2006) Masterpiece
Jyu-Oh-Sei (TV) Decent
Jormungand Perfect Order (TV) Excellent
Jormungand (TV) Excellent
Jin-Roh - The Wolf Brigade (movie) Bad
ItaKiss (TV) Very good
(The) irregular at magic high school (TV) Excellent
Iria - Zeiram the Animation (OAV) Excellent
Inu X Boku Secret Service (TV) Excellent
Intrigue in the Bakumatsu - Irohanihoheto (TV) Good
Interlude (OAV) Masterpiece
Innocent Venus (TV) Excellent
Infinite Ryvius (TV) Masterpiece
Hyōka (TV) Very good
Honey and Clover II (TV) Good
Honey and Clover (TV) Very good
His and Her Circumstances (TV) Good
Higurashi no Naku Koroni Kai (TV) Masterpiece
Higurashi no Naku Koro ni Rei (OAV) Excellent
Hi-no-youjin (movie) Good
Heroic Age (TV) Excellent
Hell Girl: Two Mirrors (TV) Excellent
Hell Girl: Three Vessels (TV) Excellent
Hell Girl (TV) Very good
Heaven's Memo Pad (TV) Masterpiece
Harlock Saga (OAV) Good
Hanasaku Iroha: Home Sweet Home (movie) Very good
Hanasaku Iroha - Blossoms for Tomorrow (TV) Excellent
Haibane Renmei (TV) Masterpiece
.hack//SIGN (TV) Excellent
.hack//Quantum (OAV) Excellent
.hack//Liminality (OAV) Masterpiece
Gunslinger Girl: Il Teatrino (TV) Excellent
Gunslinger Girl: Il Teatrino (OAV) Excellent
Gunslinger Girl (TV) Masterpiece
Gungrave (TV) Excellent
Gundress (movie) Very good
Green Legend Ran (OAV) Excellent
Gosick (TV) Very good
Good Morning Althea (OAV) Good
(The) Glass Rabbit (movie) Very good
Glass Fleet (TV) Good
(The) Girl Who Leapt Through Time (movie) Excellent
Ginga Tetsudo Monogatari: Eien e no Bunkiten (TV) Good
Ghost in the Shell: Stand Alone Complex: Solid State Society (movie) Masterpiece
Ghost in the Shell: Stand Alone Complex 2nd GIG (TV) Masterpiece
Ghost in the Shell: Stand Alone Complex - The Laughing Man (OAV) Good
Ghost in the Shell: Stand Alone Complex - Individual Eleven (OAV) Good
Ghost in the Shell: Stand Alone Complex (TV) Masterpiece
Ghost in the Shell: Arise (OAV) Masterpiece
Ghost in the Shell 2: Innocence (movie) Excellent
Ghost in the Shell (movie) Excellent
Ghost Hunt (TV) Excellent
Ghost Hound (TV) Excellent
Genshiken 2 (TV) Very good
Genshiken (TV) Very good
Genshiken (OAV) Very good
Geneshaft (TV) Decent
Gasaraki (TV) Very good
(The) Garden of Sinners (movie series) Masterpiece
Gankutsuou: The Count of Monte Cristo (TV) Excellent
Gambo (movie) Very good
(The) Galaxy Railways: A Letter from the Abandoned Planet (OAV) Good
(The) Galaxy Railways (TV) Good
Galaxy Express 999 (movie) Excellent
Full Metal Panic! The Second Raid (TV) Excellent
Full Metal Panic! (TV) Excellent
From the New World (TV) Very good
Freedom (OAV) Excellent
Fractale (TV) Good
Flag (ONA) Good
(The) Five Star Stories (movie) Excellent
Five Numbers! (OAV) Excellent
Fire Tripper (OAV) Excellent
Figure 17 (TV) Excellent
Fate/Zero (TV) Excellent
Fate/Zero (TV 2) Excellent
Fate/stay night: Unlimited Blade Works (movie) Excellent
Fate/stay night (TV) Excellent
Fafner: Heaven and Earth (movie) Very good
Fafner (TV) Very good
Evangelion: 3.0 You Can (Not) Redo (movie) Excellent
Evangelion: 2.0 You Can (Not) Advance (movie) Excellent
Evangelion: 1.0 You Are (Not) Alone (movie) Very good
Ergo Proxy (TV) Masterpiece
ef: a tale of memories (TV) Excellent
ef: a tale of melodies (TV) Excellent
Eden of the East: The King of Eden (movie) Very good
Eden of the East: Paradise Lost (movie) Very good
Eden of the East (TV) Excellent
Durarara!! (TV) Excellent
Dogs: Bullets & Carnage (OAV) Very good
(The) Disappearance of Haruhi Suzumiya (movie) Excellent
Destiny of the Shrine Maiden (TV) Masterpiece
Denpa teki na Kanojo (OAV) Excellent
Dennō Coil (TV) Excellent
Death Note (TV) Excellent
Death Billiards (movie) Excellent
Dead Girls (OAV) Excellent
Darker than Black: Gemini of the Meteor (TV) Very good
Darker than Black - Kuro no Keiyakusha: Gaiden (OAV) Very good
Darker than Black (TV) Very good
Dante's Inferno: An Animated Epic (OAV) Very good
Dantalian no Shoka: Ibara-Hime (OAV) Good
Dallos (OAV) Very good
Crest of the Stars (TV) Masterpiece
Cowboy Bebop: The Movie Masterpiece
Cowboy Bebop (TV) Excellent
Code Geass: Lelouch of the Rebellion R2 (TV) Excellent
Code Geass: Lelouch of the Rebellion (TV) Excellent
Clannad After Story (TV) Very good
Clannad (movie) Excellent
Clannad (TV) Very good
Chrome Shelled Regios (TV) Excellent
Chobits (TV) Excellent
(Le) Chevalier D'Eon (TV) Very good
Casshern Sins (TV) Not really good
Cannon Fodder (movie) Decent
CANAAN (TV) Good
Bunny Drop (TV) Masterpiece
Buki yo Saraba (movie) Excellent
Bubblegum Crisis: Tokyo 2040 (TV) Excellent
Broken Blade (movie series) Very good
Boogiepop Phantom (TV) Very good
Bokura ga Ita (TV) Very good
Blue Remains (movie) Decent
Blue Gender (TV) Masterpiece
Black Rock Shooter (OAV) Very good
Black Lagoon: The Second Barrage (TV) Excellent
Black Lagoon: Roberta's Blood Trail (OAV) Excellent
Black Lagoon (TV) Excellent
Black Jack: Child from the Sky (OAV) Decent
Black Jack The Movie Excellent
Black Jack Final (OAV) Excellent
Black Jack (OAV) Excellent
Black Butler II (TV) Good
Black Butler (TV) Very good
Birdy the Mighty: Decode (TV) Excellent
Birdy the Mighty Decode:02 (TV) Excellent
Birdy the Mighty Decode: The Cipher (OAV) Very good
Birdy the Mighty (OAV) Very good
Beyond the Boundary (TV) Masterpiece
BECK: Mongolian Chop Squad (TV) Masterpiece
Banner of the Stars III (OAV) Excellent
Banner of the Stars II (TV) Masterpiece
Banner of the Stars (TV) Masterpiece
Bakemonogatari (TV) Excellent
Baccano! (TV) Masterpiece
Arpeggio of Blue Steel (TV) Excellent
Armored Trooper Votoms: The Last Red Shoulder (OAV) Excellent
Armored Trooper Votoms: The Heretic Saint (OAV) Not really good
Armored Trooper Votoms: Red Shoulder Document - Roots of Treachery (OAV) Very good
Armored Trooper Votoms: Phantom Arc (OAV) Very good
Armored Trooper Votoms: Pailsen Files (OAV) Very good
Armored Trooper Votoms: Pailsen Files (movie) Good
Armored Trooper Votoms: Big Battle (OAV) Very good
Armored Trooper Votoms Case;Irvine (OAV) Very good
Armored Trooper Votoms (TV) Excellent
Armor Hunter Mellowlink (OAV) Excellent
Armitage: Dual-Matrix (movie) Very good
Armitage III: Poly-Matrix (movie) Excellent
Armitage III (OAV) Masterpiece
Arjuna (TV) Not really good
Argento Soma (TV) Good
Aquatic Language (special) Excellent
Aquarian Age - Sign for Evolution (TV) Masterpiece
Appleseed: Ex Machina (movie) Excellent
Appleseed XIII (TV) Good
Appleseed Alpha (movie) Very good
Appleseed (OAV) Good
Appleseed (movie) Excellent
Another (TV) Excellent
anohana: The Flower We Saw That Day (TV) Excellent
anohana: The Flower We Saw That Day (movie) Very good
(The) Animatrix (OAV) Very good
Angel Heart (TV) Good
Angel Beats! (TV) Excellent
Aldnoah.Zero (TV) Excellent
Akira (movie) Very good
Air (movie) So-so
Adieu Galaxy Express 999 (movie) Very good
5 Centimeters per Second (movie) Not really good
3x3 Eyes Seima Densetsu (OAV) Excellent
3x3 Eyes (OAV) Very good
009 Re:Cyborg (movie) Masterpiece