I like how the Arcanum companions worked, with the companions having alignments to light or dark, with your choices effecting how they like you, they will even change their stat investments a bit according to your choices.
The only problem with them is that they eventually got overpowered to the point that you did nothing during combat.
Also on another note I loved how the persuasion worked in Arcanum, where it just increased the dialogue options (with no % chance of success shown, that just pisses me off) leaving the player to figure out what the best choices are