I think Bruce Timm, on his B:TAS commentaries, has pointed out little touches here and there that the animators added themselves that he didn't necessarily ask for but liked, such as Poison Ivy doing that little back-and-forth rock with the chair after she sits down in "Harley and Ivy."
Seth MacFarlane has also pointed out such little touches in various Family Guys. The one I remember most is "To Live and Die In Dixie," when one of the hillbillies walks up to Peter and the others on the bridge and gives the body a slight nudge with his foot, knocking it off into the river. MacFarlane noted that wasn't even in the script or storyboards, but was just a funny little addition the animators made themselves.