I like Borders, they have about the best selection around, at least in my area. What type of book or magazine are you looking for that they dont seem to stock? You might have to go to a specialty store, or Borders will order anything for you.
So far Barnes & Noble has satisfied my reading addiction. I have gone in to order a book only to have them request for me to wait a minute and have returned with the publication I wanted to order
Elliott Bay Book Company, Seattle, is a terrific bookstore and my current favorite. Light years of difference between this privately-owned store and the average Borders or B&N. Huge selection, properly organized, and a very educated and helpful staff.
Unfortunately, it's in Seattle and I'm in Kansas City...
I haven't honestly bought a print book in a couple years... I have 5000 + fiction books on my PC... most of them I buy online from places. Mostly Science Fiction... Baen.com has tons as well as a free library with tons of books from GREAT authors.
Borders and Barnes & Noble are OK. I enjoy Half Price Books pretty well. I got the entire John Carter of Mars series in paperback for around $3, plus the rest of the Tarzan novels I didn't have.