I' d forgotten about Yesterday's Enterprise.
Re: Parallels, I personally wouldn't count it, nor would I count the Fringe episodes set in or dealing with the ' Red- verse' or anything from Fringe' s fourth and fifth seasons, but others might.
I know Smallville had a number of alternate-reality eps, but I haven't seen any of them, although I'm really intrigued by Noir and Apocalypse.
Edit: I also wouldn't count any of the SG1 episodes that dealt with alternate universes. SGA's Vegas definitely counts, though.