Those are the three I tend to use for my manga 
and dvds.

Planet Anime-- has storefronts in Houston and 
Plano, and a website at www.planetanime.com ; I 
get my manga from them, although if you live in 
Houston/DFW, you can rent stuff, too.

Amazon.com-- I did some pre-ordered DVDs from 
them, but you could just as easily go to bn.com 
or anywhere else.

Ebay-- It offers bootleg DVDs and legit ones. I 
swore off bootlegs after I watched a really lousy 
job done on X 1999. -_- Now I just buy the 
licensed stuff from them; you can get used DVDs 
relatively cheaply.

Warehouse Music-- Another good place for used 
DVDs. I got my Kenshin OAVs from them and some 
other good ones. You need to be careful, though; 
I bought a used DVD that ended up unplayable when 
I got it home. Save your receipt until you watch 
it, or give it a test run as soon as you get 
home. ;o)

Suncoast-- Pretty common in the malls. Most music 
stores are getting anime sections, so poke around 
whatever you have.

Fansubs-- Still available. Find a fansub distro 
webring, or go to www.fansubs.net to see who's 
subtitled what. If something has had a US company 
buy the rights, the ethical thing for fansubbers 
to do is to pull the title from distribution. So, 
in that sense of the word, I shouldn't be able to 
find, say, Ruroni Kenshin, Mononoke Hime, or 
Rayearth at a fansub distro site anymore, but I 
should still be able to find, say, Legend of 
Basara, Marmalade Boy ep. 25+, and Violinist of 
Hameln available. You can also download fansubs 
from computer sites. A friend of mine gets most 
of his new anime that way.

But for the most part, if you're looking for 
something specific, you might plug it into a 
search engine and see what you come up with. ^_^

Good luck,
-Cres