With two main outlets for DVDs (at least for me) there is a choice for new releases. Cost can be a factor. But if both stores have the same cost. This is where extras come in. Not the extras on the DVD, but item that come with the DVD. Here are a few examples.
Superman: Doomsday DVD
At Best Buy they had a Justice League: New Frontier mini comic book attached to the DVD.
At Circuit City they had a poster of one of the Death Of Superman comics.
Family Guy DVD
At Best Buy they had a Exclusive Animated Art of the DVD cover.
At Circuit City they had a little bit lower cost.
Smallville Season Six
At Bust Buy they had a mini visual guide to Smallville by DK.
At Circuit City they had it on sale, not sure if it different.
The ones above were the ones I recall from today's trip to the store. They did something similar with the Ghost Rider DVD and Heroes.
One thing I will point out is look for the sticker on the DVD saying the item is in or on the package. They the standard ones and the special one mixed together. Make sure you pick the right one.