The Neon Genesis Evangelion manga was first published in 1995 by Kadokawa Shoten Publishing Co., Ltd., with English translation rights belonging to Viz Communications, Inc.
The manga is arranged in stages, which are later compiled into books.
Up until the end of Volume 7, there were no less than four ways to collect this manga: English graphic novels, Special Collector's Edition graphic novels (unaltered sound effects and unflipped artwork, with slightly different translation in references to left and right), and equivalents in a monthly "comic book" format. Volume 8 and up were published only in unflipped graphic novel form.
The stages' titles so far that I know of:
Book 1
Synopsis: Shinji arrives in Tokyo-3, and is coerced into agreeing to be the pilot of Artificial Human Evangelion Unit-01. He goes into battle, and things go awry.
Stage 1: Angel Attack/Shito, Shuurai (2nd Angel Sachiel) - I think this book does a great job of introducing Shinji's character, compared to the anime intro.
Stage 2: Reunion/Saikai - Shinji and Gendo 's strained relationship is the focus here, and again the manga gets more in-depth than the anime did.
Stage 3: Unit-01, Lift Off/Shogouki, Lift Off - This one didn't strike me as being much different from the anime, although being still-images allowed me to get a better look at the feelings conveyed by the characters' facial expressions.
Stage 4: Silence.../Sanmoku - Not much character development here--it's primarily action. More detail is shown in the fight scenes, presumably because they don't have to worry about drawing hundreds of frames full of detail on a schedule.
Stage 5: Angel Fire/Hikari no Fuchi ni Mitamono - More action.
Stage 6: I...Cry.../Boku Hanaku - This stage seems to be wrapping up details to set the stage for later books. I particularly enjoyed the depiction of Misato's personality here.
Book 2
Synopsis: Shinji moves in with Misato, and starts at his new school. He is quite popular because of a rumour about him being a pilot, but one classmate, Touji Suzuhara, holds a grudge. Another angel attacks, and Touji and his friend Kensuke Aida wind up in the entry plug with Shinji.
Stage 7: Closing Hearts/Tojiyuku Kokoro - This one didn't seem to be very significant (except for the introduction of some new characters) until it got to Shinji's monologue at the end.
Stage 8: Shinji's Bad Mood/Shinji go Kizan Naname - This one was nifty mainly due to the conflict that appears between Shinji and Misato over Shinji's attitude towards death. I like how Shinji seems to be more of a sarcastic-apathetic, instead of the passive apathy he showed in the anime.
Stage 9: The Trials of a True Fan/Mania no Junan (3rd Angel Shamshel) - Yay, more action!
Stage 10: Shonen and Knife/Knife to Shounen - Mostly action, but it manages to set up more conflicts between Shinji and Misato to be developed later.
Stage 11: Third Child Wandering/Samayoeru Third Children - Shinji and Misato's disagreements boil over when Misato gets fed up with Shinji's smart-alecky attitude. Add in some depressed Shinji monologue and Kensuke strangeness, and it makes for a good bit of manga.
Stage 12: Fumbling Towards Kindness/Yasashi Sano Katachi - While Touji and Kensuke develop a bit more, Misato reveals a lot about her motives regarding living with Shinji and Pen-pen.
Book 3
Stage 13: White Scars/Shiroi Kizuato
Stage 14: The Warped Room/Yugakuda Heya
Stage 15: What Her Crimson Eyes Believe In/Akai Hitomi no Shinjirumono wa (4th Angel Ramiel)
Stage 16: Abandoned Memories/Suteraretaki Aku
Stage 17: The Night Before Battle/Kessen Zen ya
Stage 18: Blood Battle/Kessen!
Stage 19: The Moon Inside the Darkness/Yumi no Naka no Tsuki
Book 4
Stage 20: Asuka Comes to Japan/Asuka, Rainichi (5th Angel Gaghiel)
Stage 21: The Uninvited/Manekare Zarumono
Stage 22: Asuka Attacks/Asuka Attack (6th Angel Israfel)
Stage 23: Try, Try Again/Try Again
Stage 24: Dissonance/Dissonance
Stage 25: Shall We Dance?/Shall We Dance?
Stage 26: One Moment, One Heart/Shunkan, Kokoro, Kasanete
Book 5
Stage 27: The Party
Stage 28: Follow Back, Along Your Scar
Stage 29: Centopath
Stage 30: Catch the G-Shock (7th Angel Sahaquiel)
Stage 31: Nerv Blackout
Stage 32: The Abyss of Truth
Stage 33: Aquarium
Book 6
Stage 34: The Fourth Child
Stage 35: Light, Then Shadow
Stage 36: Confession
Stage 37: The Gift (8th Angel Bardiel)
Stage 38: Ambush
Stage 39: The Dummy System
Stage 40: Staining the Twilight Black
Book 7
Stage 41: Fist
Stage 42: Ashen Skies
Stage 43: Cross-Examination (9th Angel Zeruel)
Stage 44: Atonement
Stage 45: A Man's Battle
Stage 46: The Awakening: Part 1
Stage 47: The Awakening: Part 2
Stage 48: Eradication (10th? Angel Tabris)
Book 8
Stage 49: ...Kiss
Stage 50: Into the Heart
Stage 51: Mother
Stage 52: Flashback
Stage 53: A Giant Made of Light
Stage 54: The Birth of Nerv
Stage 55: Message
Stage 56: Of Jealousy
Book 9
Stage 57: The Fifth Child
Stage 58: Rejection
Stage 59: Pride
Stage 60: A Doll
Stage 61: The Spear of Longinus
Stage 62: Distance
Stage 63: Returning Fire
Further information on book 10 (and any books afterwards) will be added when I find them. Information on the original Japanese titles for books 1-4 from http://www.anime-archive.net/.
NB: The numbers of the angels on this list do not match the numbers in the bios they link to. The manga uses a different numbering system, shown by Fuyutsuki referring to Sahaquiel as "seven" (Stage 30), and the other numbers here are based off of that reference.