I would suggest checking out the companions in Planescape: Torment, Mask of the Betrayer and Dragon Age: Origins (if you haven't already). They can be profoundly influenced, "hardened", and offer more than just fluffy banter: they can empower the PC and vice versa. Does anyone recall the Circle of Zerthimon with Dak'kon? Nothing beats that, imo. The extended dialogues with Morte and Grace were evocative, too. That's all the more impressive considering PS:T pioneered the idea of companions being more than just mules, meatshields and "banter posts".
For NWN, I especially liked Deekin and Valen; and mod-wise Dante and Robert of The Aielund Saga were great, even if simple. I also liked how you could influence Zarala's alignment in Swordflight.