Thinking of actual DVDs and not things like games and books, I'm surprised that no one mentioned Tsutaya (or is it not popular in the Kanto area like it is in the Kansai area?).

Book-Off does have some DVDs, but I have noticed that their prices are not that cheap, even if the quality is pretty good (they rock for books and games, but not so much for DVDs).

Big electronic stores also tend to have a decent selection of DVDs (like Big 5 Camera). I second the idea of taking a trip to the Akihabara district in Tokyo, although that might present more video game, figure, etc opportunities than DVDs.

Mandarake, as far as I know, does not carry very many DVDs at all. At least the two stores in the Osaka area that I have been to are mainly manga, figures, cels, cosplay, and doujinshi.