Improving Alignments

[Psychic Robot]

The easiest way to improve D&D alignment is to toss it.  I could write a whole essay on how Law and Chaos work together with Good and Evil to form a character's moral framework and how characters should treat alignment in the game, but the best way to deal with alignment is to junk it.  Keep it for things like holy and anarchic weapons, but disregard it for everything else.  Instead, I'd recommend having the players answer the following questions:

1. What are three things that your character believes are morally wrong?  Why does he believe this?
2. What are three things that your character believes are morally right?  Why does he believe this?

Based on the answers, you can probably formulate a guideline for alignment.  If the player lists something like slavery as being wrong because "it just is," then you're probably dealing with a Chaotic Good character--he doesn't have an overarching code; he goes with what he feels about a situation.  If the character says that slavery is good because "the weak should rule the strong," then you're probably dealing with Lawful Evil--he's evil, and he has a set moral framework.

[Vinom]

The easiest way to improve D&D alignment is to toss it.  I could write a whole essay on how Law and Chaos work together with Good and Evil to form a character's moral framework and how characters should treat alignment in the game, but the best way to deal with alignment is to junk it.  Keep it for things like holy and anarchic weapons, but disregard it for everything else.  Instead, I'd recommend having the players answer the following questions:

1. What are three things that your character believes are morally wrong?  Why does he believe this?
2. What are three things that your character believes are morally right?  Why does he believe this?

Based on the answers, you can probably formulate a guideline for alignment.  If the player lists something like slavery as being wrong because "it just is," then you're probably dealing with a Chaotic Good character--he doesn't have an overarching code; he goes with what he feels about a situation.  If the character says that slavery is good because "the weak should rule the strong," then you're probably dealing with Lawful Evil--he's evil, and he has a set moral framework.

What if you had a character who wanted to kill off all humans "Because the world better off without us" is that evil, or for the greater good?

[Zeke]

I think it's OK to mostly ditch alignment in D&D. However, there are parts of the system (various clerical spells, and magic items) which work off of this mechanic. So you either need to patch that mechanic with something else, or keep alignment for this purpose but otherwise ignore it.

[Psychic Robot]

What if you had a character who wanted to kill off all humans "Because the world better off without us" is that evil, or for the greater good?

Generally, whenever someone starts doing something for the "greater good," it's evil.  (If you have to justify why you're doing something, there's a good chance that you shouldn't be doing it.)  However, the problem is that the character's intent seems to be good, and his sanity is in question, and both of those things matter when dealing with good and evil.  For that particular character, I would say Neutral Evil with True Neutral tendencies--his ethic is very broad, so it's in between lawful and chaotic, and while his deeds are evil, he seems to be a pragmatist when he's not murdering civillians, indicating that his other actions may be deemed good or evil depending on whether or not he deems the course of action as logically sound.

[Vinom]

(If you have to justify why you're doing something, there's a good chance that you shouldn't be doing it.) 

A doctor might have to justify letting an evil man die on the table, or justify healing him... which act is evil?

I actually had a Lawful Good Paladin Mongrelfolk who tryed to "Rid the world created by the gods of this infernal human infection"... he had a lawful good god and lord backing him up...

[Psychic Robot]

A doctor might have to justify letting an evil man die on the table, or justify healing him... which act is evil?

Note that I said "there's a good chance" that it's evil, not that it always means that it's evil.

I actually had a Lawful Good Paladin Mongrelfolk who tryed to "Rid the world created by the gods of this infernal human infection"... he had a lawful good god and lord backing him up...

Genocide: Lawful Good since 1942.

[Vinom]

I actually had a Lawful Good Paladin Mongrelfolk who tryed to "Rid the world created by the gods of this infernal human infection"... he had a lawful good god and lord backing him up...

Genocide: Lawful Good since 1942.

Humans: Usually Evil since 4500 BC (or any other date of creation)