Alignments and Orders

PCs are Aligned or they don't have any kind of alignment at all (unaligned or whatever).

ALIGNED

Aligned characters have sworn to align themselves with a creed, goal, organization and/or ideal.

Creeds, Goals and Ideals are meant to be a statement or a short list that summarizes the conduct or beliefs the characters values most highly in herself and others. The terms, "creeds, goals, and ideals" are meant to indicate a devotion that, by its nature, highly and broadly impinges on a character's lifestyle. The terms are not used prescriptively: "Bushido" is certainly a creed, but the category could include, "a Devotion to the Rusted Heart of Vorn" as well as, "Sworn to the Dug of Lady America," and also, "Believes in Knightly Virtues," and also, "Lawful Good" or "True Neutral," etc, etc. The choice ought to be cleared with the GM, but broadly should significantly impact character lifestyle. Anything less is "unaligned but with beliefs." Most of this stuff is either already in the player's head or is something that arises out of play. Either source is great.

Organizations are things like orders (religious, monastic, warrior or otherwise), guilds, lodge, confraternities, sororities  bands, tribes or any other social construct that has established rules of conduct and etiquette.

None of these are necessarily mutually exclusive (Evil Samurai: Lawful Evil, Follower of Bushido, Member of the Lodge of the Rotten Lotus), but the more of these the character has, the more they're limited by their oaths. 

Characters can start out aligned or can pick up an alignment during play, usually as the result of something major happening to the character or as part of the process of the character joining an Organization. Other than the most simple "conversion," the actual process will vary widely, but will nearly always involve an epiphanic experience and then a more prolonged process of joining the group/being mentored. Starting characters that begin aligned usually won't hold membership in an Organization (perhaps, with the exception of Clerics of a particularly monastic or monomaniacal bent).

HOW IT WORKS

YOU GET POINTS, CHIPS, WEDGES OR SOMETHING

I use points. When a character acts in accordance with the dictates of her alignment, she may earn an "alignment point." Likely no more than one is earned per session and the range here is just from zero to three. If a character earns an alignment point, the player should note it on the sheet and write down a couple words about how the point was earned. I award points at the same time as XP (ie, at the end of the session), but whatever.

Acting against one's alignment generally results in an immediate loss of at least one point.

Instead of points, you can come up with some other metric, ideally one that is tailored a bit to the alignment in question ("oh man, I finally got three Nurgles!" or "Awesome, now my Cthulu is totally colored in"). I like the level of granulation I get from 0-3, but maybe more would work better for you (might be especially useful in campaigns oriented strongly towards aligned characters).

BUT YOU CAN'T USE THOSE POINTS
These points don't translate into anything a Player can pull out and use, but they do indicate to the GM how closely the character has been cleaving to their chosen alignment. A higher score likely means access to more stuff. A highly Lawful Good Fighter might get invited to join an order of Knights Mendicant (and maybe get to become something like a Paladin). A highly Evil Fighter might get an invite to a Chaos Cult or a Assassin's Guild. Deities may take notice of the highly aligned and deign to send signs or messengers to provide quests or even provide boons. Importantly, none of this stuff comes without strings. Not only do you have to act in a certain way to get the points, but the interesting thing that might come from having those points will have some kind of cost or ongoing risk associated with it.

Carousing while aligned will often yield strange and interesting results.

ORGANIZATIONS (ORDERS, LODGES, GUILDS)

Joining an Organization will likely involve time for contemplation, a specific cost and perhaps the performance of certain tasks. Order membership usually comes with a number of perks and services; there is a relatively corresponding cost to join. One of the costs is always adopting an alignment or code or creed (likely one of the latter two).

Time for Contemplation

Can mean time for reflection, devotion and contemplation; may be solitary, may be communal, will almost certainly always be spent with like-devoted people. Could still be spent during rest time at camp; while everyone else is researching spells, poisons or getting fantastically drunk; or even on the march ("cleric, teach me they ways"). It might also be as simple as reading a trusty, dog-eared, book like the Enchiridion or Sir Marveaux's Primer on Conduct Becoming a Knight.

Specific Costs

These might be a large donation, evidence of certain social status (owning land, retaining certain employees), a pledge to tithe a significant portion of future income, or certain, special items (a very well made knife, a jade frog, a breastplate painted green). The GM will likely have ideas here but might solicit input from the table. These may be associated with certain tasks.

Certain Tasks

"Bring me the skull of a virgin," "bring me evidence you have been chosen by our deity," "Bring me a black breastplate and the blood of a lecherous unicorn." These can be simple fetch quests, but really ought to be more cryptic and thematic. If there is a specific location required, it should be only a day or so away. If there is a thing to be brought it ought not be something you can buy over the counter somewhere in town.

Everything in between will require a character's time and perhaps also tasks and costs in some combination. 

pictures: Antrhopofagy Chronicles 1 by Atanasio, still from Ghost Dog: Way of the Samurai