I'm looking for manga where the heros are shunned by the people they protect.

Where they're thought of as evil/monsters/dangerous/troublesome/etc and are shunned, unwelcome, and/or outcasts.

Like they're treated as the lesser of two evils and are needed to keep the other greater evil at bay.

A prime example of this is claymore and I think possibly this newer manga I read recently trace maybe even gunslinger girl

They just have to not be treated as humans. Less than human. Unwanted but needed.

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Feed your head.

Akumetsu?

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Perhaps Pluto. Some people like the robots, but others consider them second-class citizens, just tools and/or weapons.

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Avatar by tassyn.livejournal.com

Reading: Kingdom, Sangokushi, Historie

I don't know if it will suits your tastes, but perhaps Riki-Oh. The main character is often called a monster or a beast, but (dealbreaker?) the focus is usually on killing his enemies and rarely about protecting somebody.

Superior - happened somewhere in the middle of the series
Junk - Record of the Last Hero - kinda fit but they are not really needed anyway...

if my memory serves me right, Violinist of hameln has this kind of scenario as well.

definitely second Ubel Blatt

and maybe 666 Satan- except he isn't shunned/hated by every person per say

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Top 3 favorite manga right now:
3. Ao no Futsumashi
2. Wolf Guy
1. Ubel Blatt
!!!!!

Asklepios

Maybe?

There are actually a lot. Here are some :
Berserk
Dangu
Nephilim John
Pilgrim Jager
Priest

cant believe no one mention Angel Densetsu the hero's face is so hideous but actually is a nice guy and usually misunderstood by people

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well i don't think hes all that needed... it'd probably be for the best if he didn't exist in the first place <_<"...

Trigun is a good one though, i think, i forgot if hes needed though... might be like my description of angel densetsu =|...

Vampire Juujikai

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What I like in Trivial Pursuit style. Pick your category:

Megalomania sort of sad.

i suggest Crimson Grave...

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Ras tel ma scir magister Veniant Spiritus Aeriales Fulgurientes!! Cum Fulguratione Flet Tempestas Austrina, Jovis Tempestas Fulguriens!!!

I'm not really looking for heros who are viewed as villians.
ubel blatt everyone thinks of him as a bad guy/villian when the truth is different that what they believe.

I'm looking for something more along the lines of everyone knowing that the existence of the "heros" are necessary, but rather than praised/celebrated/welcomed(how heros are normally treated) the people they protect are prejudice against them and shun them.

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Feed your head.