In my opinion, the very concept of a home media room (home theater room) derived from the time-hallowed tradition of having a whole room in the house dedicated to books, that is having a home library. Such a room necessarily demanded some space assigned where you can enjoy the books: with desks, armchairs and other kinds of comfortable seating solutions. Now, remember that books are properly considered to be media, just as movies and music (which you should know if you ever used media rate to send books or CDs by USPS). It is natural then to also have special storage in your media room to house your collections of CDs and DVDs. There is a small complication, however.
Firstly, DVD and CD covers are usually quite colorful, much more so than book covers. This creates unwanted distraction even when the light in the media room is turned off. Also, because DVDs and CDs generally do not differ much in terms of their size this results in rather monotonous looking shelves of boxes, a problem hardly alleviated by the presense of boxed sets.
Secondly, a decent home theater requires good accustics. Numerous plastic boxes are not likely to achieve this.
What's the solution? It seems as if you really want to have enclosed shelving. If possible, these storage units should also have additional padding, to prevent the sound from getting trapped the room, causing dinny sounds and undesited reverb.