It can be carried out by the protagonist or completely without his knowledge and consent. Not exactly looking for secret identity, more like no identity.

No examples. In Nononono, she is supposedly died, and is living as her brother. That doesn't fit perfectly, since she took over someone's life. MuvLuv Unlimited is more like it, where he isn't supposed to exist and has a fake identity, but it was bc it was a different world, and there was no death involved. And I think that changes later on.

No ghosts and try to stay away from supernatural.

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"I'll shut your mouth~~~~~ with mine~~~"

二息歩行

I know that Silver (FUJITA Kazuko) would fit your description, she had another alias however everyone believed she was dead. I've read it once and wouldn't mind reading it again, that is the only one that I know of so far that has a faked death.

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High above the tree tops.

Gunslinger Girl??

Urasawa's Monster and 20 Seiki Shounen have a lot to do with identities and trying to erase identities etc.

Pretty Face he supposedly died, but got saved by a professor who reconstructed his body based on a photo, sadly it was one from his crush... so he has to take over as her twin sister, it's like your first example

perhabs Claymore after time skip the whole team is said to be dead, doesn't have supernatural criteria, but still...

Maoyuu Maou Yuusha he fakes his death to help the demon lord, like above, far from realistic...

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in need of romance?
uncommon, sad, sweet

jesus- though the titles lame, quite interesting, the manga style is a bit old but its good,

Mademoiselle Butterfly. Wasn't really "on purpose," but not by accident either. Sweet. Made me cry every time. But it's good.

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"'The lives I've taken will be paid for with my own life.' That's one way to look at it...but it doesn't mean they come back once you die. Lives can also be paid for by the sword; by redeeming yet other lives. That is why 'Hitokiri Battousai' is still alive in the Meiji Era."

don't click this link...

You don't meet him right away, but a character that ends up being important in Tetsuwan Girl fits this description fairly well.

Mm, many characters in Detective Conan fake their death...

Code Geass doujinshi - Lilith http://www.mangaupdates.com/series.html?id=58276
Without the main character's knowledge and consent. Yaoi.

Nanatsu no Taizai Their group of 7 was supposedly wiped out but they're still alive.

Yuureitou

07 Ghost too many characters to mention.

Edit: 300th post! woot.