For new anime goods I recommend Animate's main 
store in Ikebukuro. There is also a K-Books store 
right next to it which sells second hand anime 
goods. There is a Gamers around there too but I 
didn't manage to get to it.

Gamers and Animate in Akihabara are great too. I 
found the smaller Gamers near the train station 
had more anime goods than the main store. The 
main store had a lot more manga.

For cels I've only been to the cel stores in 
Nakano and Commit in Akihabara.
The Commit store was a real #$%&$# to find. It is 
a ssmall shop up some non-descript stairs with no 
signs on ground-level.
I found some cels in Mandarake, Shinjuku but they 
were cheap lower, quality cels.

Anyway, I recommend the following site for maps 
and locations to anime-related shops.
http://www.cuso4.com/guide/

It is very up-to-date and was VERY useful on my 
recent holiday in Tokyo.
Hope this helps.
- X