The specials stand out for me more than any of the stand alone episodes. There have been a few normal episodes where "things go wrong" and the 3 of them act surprised that something bad could have happened, but it just seems too planned and awkward for me.
The one thing that stands out for me is the camera work and editing, usually when they are reviewing cars. It's so slick, cool and accompanied by great tunes too that I usually just tune out what Clarkson is yammering on about.
Favourite episode of mine would have to be the Vietnam special. They weren't as annoying as usual (though they still had their moments) and some of the shots were stunning.