I keep mine in their boxes and put those in plastic protectors (just the cheap thin ones, not the thick, solid acrylic ones), and have them stacked on top of one of my dvd shelves... I have almost 1,100 dvds so there's loads of rooms on top of all the shelves I need for those
I must admit that after seeing peoples collections out of the box, I think keeping them in is the right decision - I actually prefer the way they look in the box, by a BIG way!