I haven't been to the El Cajon one, but I've been to the Ocean Beach one a few times. The prices are pretty decent on PS2/Xbox stuff. They had Tales of the Abyss for $30. I would have bought it if the cover wasn't sun damaged (it was out on an endcap by the front window). If you go older, they tend to be much more expensive than ebay. For example, I think Hoshigami on PS1 is like $30-$40 or something, and cart only Secret of Mana was somewhere in the range of $50? This is of course, my experience.
Also, there's another video store called Games On in PB. I don't know how it has such good reviews on Yelp. They must have been friends or paid for the reviews. They're super expensive. More than Best Buy or Gamestop. For example, I'd expect they'd have Borderlands at $60 there right now, since the last time I went in a few months ago, Metal Gear Solid 4 was $60.