At the moment in the game, the best alignment by far is True Neutral. Almost all min/max builds have it, since it has the most advantages- no negative levels, easy access to holy/anarchic/axiomatic weapons, and slightly restricted access to pure good/law/chaos that can be more or less easily bypassed by a UMD score. Annoying enemy alignment-based spell effects don't work as well or at all, and the only builds I have seen that go for an alignment besides TN either did so for flavor, rp, or was a monk or paladin. People need a greater incentive to actually choose an alignment.
My suggestions -
Make holy like pure good (damages neutral characters, requires a higher umd score than pg), or, to avoid rendering someone's weapon useless, implement a attribute that was similar to pure good but does the same or more damage as holy.
Same as above, but for anarchic/axiomatic
Start dropping some good-aligned gear! What with supremely powerful evil items like the Litany causing negative levels to only good-aligned players, there should be good equivalents that punish users for their neutrality (or simply not be usable by non-good players).
Implement more quest mechanics based on alignment. Want to get that extra chest for the optional? Have the chat box only give the side-quest of saving the innocents to a good player, the option to steal back the priceless artifact to a chaotic character, or the option to capture the criminal alive to the lawful character. Make a quest more rewarding to someone who doesn't just take the easy way out when it comes to alignment.