Well, Nakano Broadway is one of the best places
for shopping for anime cels.  Besides AWS and
Mandarake, also check out the 2nd and 4th floors
(reachable by the stairs).  Anime Shop Commit is
on the 2nd floor, and there's also Anime Shop
Zero/what ever its current name is on the 4th floor.  

AWS has their main store on the 3rd floor, and
their adult cel store on a side hallway on the 3rd
floor.  Mandarake has their cels on the 4th floor.  

Other than that, I can't really think of anything
good--  Commit once had a branch in Akihabara, but
I believe they closed it down.  Same goes for AWS.
 Mandarake in Shibuya also has a few cels, but not
many.  Animec in Shinjuku (Shinjuku-sanchome
subway station) had a few cheap cels (didn't stop
by there when I was in Tokyo last year, so I don't
know if they are still there).  

In Osaka, check out Panic Media Mix-- it's just
like AWS.   Also, if you happen to be in Tokyo
when they're having a Takarajima Collection Market
at Tokyo Big Site, you can find a lot of cel
collectors/dealers there.  Unfortunately the next
Takarajima is Aug 22 in Nagoya or Nov 14 in Tokyo.
  There are a few other small anime cel stores in
Tokyo, but nothing really recommendable.