But one thing I do to attempt to do is, I advise the players to start out as neutral and allow them to change their alignment over levels according to their actions in the game, but some classes require a certain alignment [paladin, cleric] so outside of said classes, I do ask for neutrality it makes things so much faster at startup, and startup seems to be the most nerve racking and annoying part of D/D [we're all inpatient]

And the allegiance system from Fantasy Concepts http://www.lulu.com/content/1444818 which is the best way to handle paladins and other fervent types.

The Basics of Allegiance
A character may have up to three allegiances, listed in order
from most important to least important. These allegiances
are indications of what the character values in life, and may
encompass people, organizations, or ideals. A character will
rarely have no allegiances (as a free spirit or a lone wolf will
almost always have a single allegiance to Self), and may
change allegiances as he or she goes through life. Also, just
because the character fits into a certain category of people
doesn’t mean the character has to have that category as an
allegiance. If the character acts in a way that is detrimental
to his or her allegiance, the GM may choose to strip the
character of that allegiance (and all its benefits) and assign
an allegiance more suitable to those actions.

Pledging Allegiance
A hero’s allegiance can take the form of loyalty to a person,
to an organization, to a belief system, to a nation, or to an
ethical or moral philosophy. In general, a character can
discard an allegiance at any time, but may only gain a new
allegiance after attaining a new level.

I currently play a rogue who is a ‘good’ guy. However, through his back story he’s realized that he is very good at killing people. He finds it easy and enjoys it a little more than he should. This thought terrifies him as he realizes that he could become a murderer. These shades of grey that he has bring him to life and allow me to enjoy role playing him.

Personally, I prefer to describe characters in terms of the colours of Magic: the Gathering, since that system does a much better job of capturing the characters motivations and means of achieving their goals. It also has the benefit of being extremely subjective (as compared to the objective alignments of DnD). (Also, a colour alignment reveals much more to a DM on how to design hooks for a character.) The main downside is that the system is a lot harder to explain, and a player needs to really understand the motivations of each of the 5 colours before they can really know what their character is (so a lot more prep work).

[I do note that although I like alignment itself as a simple, vague system, I do NOT like Detect Good/Evil/Law/Chaos, as I do not like the idea of directly tying the alignment components to the Outer planes.]

I encourage my players to pick alignments, but we don’t pay close attention to them. Often, my players don’t know exactly how they want to play their characters, so they’ll pick an alignment that feels right, then after a few sessions, will change it.

Which is perfectly fine. It’s a role-playing aid.

I’ve always treated the alignments this way:

“How willing is your character to follow rules?”
Willing = Lawful; completely unwilling = Chaotic
“Does your character help others all the time, or is he selfish?”
Helps others = Good; selfish = Evil

That’s not a perfectly accurate definition of the alignments, but it gets at the point, I think: how does your character act?

If you can balance it so that people aren’t penalised for choosing a given alignment (or at least don’t become irrelevant), but that there’s a distinct difference that stems from it… Well, I’d go into that dungeon.

I once had a DM (excellent otherwise) who claimed EVERYONE was Chaotic Neutral. Hmm.