Let me refute this:
Alignment based damage eg. Holy weapons
get rid of it, or make it relevant only for undead or demonsAlignment based damage reduction eg. DR 5/good
get rid of it, or make it relevant only for undead or demonsHoly water and other alignment based consumables
make it work on undead and demons regardless of alignmentClass alignment restrictions eg. Paladin
get rid of it, restrictions based on code of conductDetect alignment spells
goes away, or change to detect unholy or whatever you want to make demons/angels/undead. (these don't even detect non-outsider alignments, only auras or intents in human/oids)Protection from alignment spells
same as aboveHoly Word and similar spells
change it so it only affects demons or undead, or get rid of itHoly Aura and similar spells
same thing, get rid of it or change itConsecrate/Hallow and similar spells
same thing, get rid of it or change itPaladin class features eg. Smite Evil
same thingSpell restrictions eg. Lawful Good clerics summoning Chaotic Evil creatures
ignore. or just not give the spell to the cleric/creatureAtonement restrictions
without alignment, what's there to atone? make it relevant only for clerics/paladins or w/ever, which it almost is alreadyMagical item effects keyed to alignment restrictions
get rid of them or change them[/quote]
it's a significant homebrew adjustment. Ultimately the game you play at your table is yours to do with as you wish, and nobody can tell you how you should run your game. But I dispute the claim that removing alignment means just "two spells stop working." You fundamentally alter the game balance with a change like this. I hope you can see that saying "nothing special" happens when you remove alignment is wrong.
You miss the point entirely. A spell is not a rule, it's a thing. A class is not a rule, it's a thing. A monster is not a rule, it's a thing. Adding or removing things is not houserule/homebrew, anymore than adding or removing castles is not a homebrew (playing Forgotten Realms without the city of Waterdeep is not a houserule). A houserule is saying: people fall unconscious when they're at half HP. Or, instead of half damage, a saving throw always avoids all damage. Those are rules. Saying "no holy weapons in this setting" or "no spells that grant flying", is not a homebrew houserule. Like inventing a new metal called Schwartz and giving some creatures a DR/Schwartz is not a houserule. Or adding "slime damage" to the list of damage types like acid, sonic... holy... etc.
Yes, removing the Alignment is a homebrew choice. But removing problematic spells that are problematic or incompatible is not, because you could do that regardless of whether you removed alignment or not!
If you don't want to remove alignment, I could just say:
"all non demons/undead/angels is true neutral regardless of ethos or cultural customs or classes, also any class can be true neutral. Also alignment doesn't dictate behavior and behavior doesn't change alignment". Your paladin still does good things, and is punished for doing bad things, but since he wasn't born an angel, he's True Neutral. There. Some angels can be dicks, and some demons can be rational, and they won't change alignment. No houseruling necessary, and all spells and effects work with no change.
EDIT: Actually, homebrew and houserules are different things, the former just meaning "not published", in summary: anything that you made. Even a map. Under that definition, a made up dungeon map that isn't published as part of a setting is homebrew, as is a custom class or spell. A houserule is actually changing mechanics. So yeah, good luck not homebrewing...