I like having small choices you can make in dialogue, but only occasionally. And, likewise, the options (imo only two) should both be something that would be in character to say.

As in, you don't get the choice between being a nice guy and a jerk, but you could chose between being a big jerk or inconsiderate. Or pick whichever one you found funnier.

I'm not a big fan of having the choices affect the storyline though. I usually tend to look down the line at the long term implications of any choice I make (in real life and games), so having choices affect the plot usually amounts to me trying to read the developers minds, as things usually have repercussions you can't possible predict.