DR Ben, I still find J&R a fascinating place to visit once a year or so. Last time I was in there (yikes, I think it was way more than a year ago), they had quite the little LP department, both new and vintage. And though it looked like everything was being sold at list price, the DVD/Blu-ray room stock was very impressive.
B&Ns might seem sterile, but a couple of the largest ones are still nice. In particular, I supposed it's out of the way for most everyone here, but the Paramus, NJ store is not only a large one, it also contains the Annex for used and bargain books. I think that Annex is what used to be across Fifth Ave. (at 18th St.) from the original store. I've found a fair number of interesting things that had slipped under the radar out there in Paramus. And for movies, they're still our last best hope.