Adam M. recently posted a good piece on deferring the choice of alignment. The idea contained in that post, as I understand it, is mostly narrative; rather than pick an alignment at first level and try to live up to it through character actions, instead make alignment depend upon low-level character actions. Presumably this would then matter somehow during the mid-game or stronghold phase of play, though the post is light on details.
Traditionally, alignment did have several mechanical effects, though only a few of them seem like they would regularly see play. For example, evil or chaotic characters should be affected by spells like protection from evil. However, these effects are few and far between, may not add enough to play for the management hassle, and anyways were largely eclipsed by the way alignment came to be interpreted as something like personality in AD&D and after.
If one is going to defer the choice of alignment, however, why not leverage incentive psychology and make attaining alignment an achievement? One could build something like a skill or feat tree with criteria, either level- or action-based, for gaining status within law, chaos, or whatever moral/allegiance structure underlies the fictional world. Action guidance could be provided by taboos or restrictions, the violation of which might cause an aligned character to fall down a rank. Alignment ranks could also be prerequisites for certain powers or faction benefits in a way that is mechanically transparent to players. Such transparency would make alignment motivational rather than descriptive.