I kinda like this...

[SangoProduction]

http://spheresofpower.wikidot.com/spirit-mender
The spirit mender is a sphere archetype for Druid. But what I really find interesting about it is how the class features are fluffed as having a will of their own. "Metal armor will fall off the spirit mender’s body as quickly as it can be put on (even over her objections)." I just find it so hillarious the mental picture of the entire party trying to suit up their fighter (who's been cursed to take a level of spirit mender), and more and more spirits just piling on.

Are there any other class features you can think of that are supposed to have their own wills and personalities? (Exclude familiars and such, since they are just extensions of the caster's will.)

[The Viscount]

Binder's Vestiges do this very prominently. Your success or failure on a binding check is what determines whether or not you are under the influence of the vestige. If you are, not complying with their influence results in stacking -1 penalty to near everything until the bind ends in 24 hours (or you expel it with expel vestige). Influences usually have a roleplay element and a strict mechanical one, though sometimes not, like with Zceryll.