Are there any series that have the protagonist confront their parent who is an enemy to the world, or develop a grudge against that parent? A daughter who confronts her mother who is suppose to be dead, or a father finds that his son turned against his country and has no choice but to confront him. I read something like this a few times, but i can't remember now. Does anyone know?

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code geass
death note ~~ do not remember if his father learned the truth.

Part of Vinland Saga

Anne Freaks is an excellent example of child vs parent, and a really great manga in general.

Grappler Baki
New Grappler Baki
Hanma Baki
Son vs. Father

I second Code Geass but watch the anime. I also second Death Note though it's not an open confrontation.

Also try
Count Cain
Angel Sanctuary
E's - Not really parent but benefactor
Fruits Basket - To a lesser extent

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The pen is mightier than the sword...and considerably easier to write with.

i remember mai hime was kinda like that at one point or another. the manga at least, the anime was a little screwy with all the lesbian action there. im not tooo much of a fan. gud plot though.

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"The man who smiles when things go wrong has thought of someone to blame it on"
- Robert Bloch

G Senjou Heaven's Door maybe kind of?

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Hrodulf and Bjornolfr, you will not be forgotten.

And if the world were black and white,
you would be my rainbow in shades of grey.

Click 'n Play!

If I had a fantasy self, it'd be a tentacle monster.

im not sure if this is the scale you're looking for, but as i recall Honey Hunt was also mother vs daughter. Her mom and dad get a divorce because of her dad's affair, but the mother (a very popular actress) is also having an affair with the protagonist's classmate, whom she likes. So the protagonist enters the show biz world to become more popular than her mother. cute guys and lots of drama ^_^ kind of a chick flick tho.

hope that helps

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"The man who smiles when things go wrong has thought of someone to blame it on"
- Robert Bloch