I just know amnesia manga^^"
The one I recently read was Tripeace. He has extreme amnesia, I don't know how it goes on but it should fit^^
Hmm, Rave also fits, but here it's a girl...
There's a memory loss arc in Gintama, but I don't think it really fits because it's just a few chapters^^"
Uhm, Phantom ~Requiem for the Phantom~ should also fit... But the manga isn't that far scanlated, I just know the anime...
Chrome Breaker... It's the girl though...

Well, I don't seem to have read many manga that fit^^"

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Zennou no noa

a mass weapon deletes the memory of a lot of people (something like tokyo)

Has Amatsuki been mentioned yet because if not it has some MAJOR mind screwing/memory loss in it (plus its a male main character)

Kuranoa [a girl loses her memories, however... But it's pretty original for an amnesia manga]
Hatsukanezumi no Jikan
Kimi no Kakera

Heptagon: If I remember correctly, it was about a girl who relives her memories to discover why she became the indifferent girl (when it comes to love) she is in the present. I really like this manga!

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NG Life

very nice and funny yet also serious at moments^^

Veins
Sabbath Cafe maybe
Umi no Aurora reincarnation
Kago no Naka oneshot, tragedy, woman lost her memory
Koucha Ouji middle and near the ending deals with memory related stuff

others:
NG x Baby typical oneshot cute shoujo
Naisho no Kaunto 5 shoujoish
Desert Storm + Silent Eye melodramatic...

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Help! I'm looking for... manga with dangerous guys http://www.mangaupdates.com/showtopic.php?tid=39874&pa ge=1#post594033

Canon. False memories.

What about Heart no Kuni no Alice? From what I'm seeing of the latest chapters, the deal with Alice being in Wonderland has something to do with her memories, that she can't remember. It's a shoujo, and it used to be labeled as psychological.

Has anyone put Rosario to Vampire Season II? This season seems to deal more with Moka's memories, as of the latest chapters.

Tasogare Otome x Amnesia - The Paranormal Investigations club is trying to find out the history of Yuuko, but Yuuko herself seems to have forgotten how she became a ghost. I think it fits. It's shounen, mystery, supernatural, and a little ecchi

Utsurowazarumono - Breath of Fire IV deals with how the dragon lord person has split apart into two people, but one of his halves does not remember being a part of the dragon lord.

Yumekui Merry is about how a Nightmare named Merry does not know how she came from the dream world to the Human world. She's trying to figure it out and meets this boy, who is the actual protagonist.

Canon -

I am really surprised that no one has mentioned Chobits! The doll has lost all her data/memories. Surely it must fit.

Déjà-vu deals with reincarnation, and lost love. I especially love the last arc, Winter, because of Park Sung Woo's art. The rest of them are all right. But i really do recommend this one.

Land of Silver Rain has a girl who loses her memories for a main character. Manhwa, but the girl can get kind of irritating.

Vampire Juujikai has all sorts of people misremembering what they saw, and the misunderstandings that arise because of those memories. I ABOSLUTELY recommend this one. It's one of my top favorites.

Id seems plausible also. Mostly there are time jumps that create memories within other people's minds that Id himself doesn't really remember....I guess this would be more time paradox than memories, wouldn't it....

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Would you like to join the Axis Order?

well you already got many recommendation.. so i just gonna add mangas that i didn't found on the thread:
ai yori aoshi the male protagonist trying to remove his harsh childhood memory, yet the girl in his past suddenly shows up
hotel the memory of an AI
ah! my goddess got some arc concerning memories (memory loss, sealed memory, block memory, etc)
school rumble Nogizaka Haruka no Himitsu kind of got the same background where the female protagonist forgot/doesn't realize that she has met the male protagonist b4 in the past... while for the male protagonist that first meeting is a cherished memory
hantsuki creating a good memory b4 the end
many more

Tomoyo After
Just 1 volume and a spin off form the main series(Clannad).

Rico is nice. She has a 3 minute memory span~~


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Adding Coelacanth, though it's a little more (or less) than just about memories.

psychic academy The main plot is all about childhood memories, and fights with psychic powers, and your usual nub hero with a natural gift for fighting that he doesn't know how to use.


And why didn't anybody mention [m]20th century boyz[/m] ? One of the best psychological mangas. It even has a live action trilogy. It has a plot too complex to make a synopsis without screwing it.