What happened to the possibility to create lawfully- and chaotically-aligned fluid (Axiomatic vs. anarchic water), as well as holy and/or unholy water?
I could have sworn it was in the game when I played 3.5... is there a reason this stuff isn't available any more?
It was, and it hasn't yet shown up in a PF product to my knowledge. To be fair, it wasn't a spectacularly useful or often relevant ability.
You may make holy or unholy water, but not other aligned waters.
Holy Water: Holy water damages undead creatures and evil outsiders almost as if it were acid. A flask of holy water can be thrown as a splash weapon.
Treat this attack as a ranged touch attack with a range increment of 10 feet. A flask breaks if thrown against the body of a corporeal creature, but to use it against an incorporeal creature, you must open the flask and pour the holy water out onto the target. Thus, you can douse an incorporeal creature with holy water only if you are adjacent to it. Doing so is a ranged touch attack that does not provoke attacks of opportunity.
A direct hit by a flask of holy water deals 2d4 points of damage to an undead creature or an evil outsider. Each such creature within 5 feet of the point where the flask hits takes 1 point of damage from the splash.
Temples to good deities sell holy water at cost (making no profit). Holy water is made using the bless water spell.
The Spell Compendium had spells that expanded upon holy water, extending it to the other alignments, but I have yet to see anything that officially does the same in PF, though in a homegame, I suspect you could probably do it without too much fuss, even one that usually sticks to official material.