Throwing my hat in the ring as pro-alignment system for 3.5e (la la la 4e I can't hear you!)
You need to respect that it's an integral part of the core mechanics of the fantasy setting. Alignment forms one of the basic building blocks for the universe. Every creature in the game has an alignment, and it's an intrinsic part of their character.
Some creatures are simply always a certain alignment, such as extraplanar monsters. Devils are always lawful evil. Demons are always chaotic evil. Angels are always good.
Player characters and other mortal creatures also possess an alignment. Mortal alignments derive from their culture, species, personal viewpoints and actions. For these creatures, their alignment is mutable but still just as binding as anyone else's. Through actions, they can have their alignment changed too, sometimes radically. For example, casting spells with an alignment description is specifically called out as constituting an act of that type of alignment. Planning to summon a bunch of devils and demons into the world? That's pretty evil, man. Smiting your foes with a few Holy Words? That's gonna earn you brownie points with the good guys.
Alignment changes are part of the game, and the rules support them happening, if failing to give a concrete system of keeping score of your alignment and when it would change. It's a DM discretion area, and I maintain that only a poor DM handwaves away the entire thing as too hard. The biggest point most of the mediocre DMs get stuck on is focusing too much on the evil and chaotic side of things. Is your Chaotic Neutral barbarian helping a bunch of villagers clear the bandit problem from the local area? Seems to me he's helping establish law and order, and his chaotic side would take a hit. Is your Lawful Neutral cleric out slaying evil monsters and protecting the innocent? Seems to me they're due to head towards a good alignment. Turning evil isn't a one-way street. It's easier, but performing good acts moves you in the opposite direction too. The trick is to strike a balance between unduly altering a player's character and recognizing the world they exist in has a system of morality that is fundamentally different to our own reality.
If you have too much of a hard time accepting that alignment in a D&D world is an objective, measurable thing instead of a subjective, indefinable quality, remember that some things in these worlds just simply work different to real life. This is a world of levels, hit points, skill points and attack bonuses. These things don't necessarily have a discrete representation in the game, but they exist and are just as valid as alignment. For better or worse, this fantasy world has a line in the sand where morality exists in nine defined flavors, and your character as well as everyone else will be in one of those nine boxes.