One store Sansui, a chain located throughout the Tokyo area, is an excellent one. It is split half fly half conventional. There are stores in Yokohama, Shibuya, Shinjuku, Ikebukoro, Ueno, Kawasaki among others. I have only been to the Yokohama, Shibuya, and Ikebukuro stores. Yokohama is the largest of the three I've been to, I believe the largest is the Shinjuku store which is the flagship. At least that is what I've read. Shibuya is two storefronts- one conventional and other fly. This store is small and cramped although the selection is still pretty good. Ikebukuro is small as well but is one combined store.
To get to it get off the Yokohama JR station and walk the direction away from Sogo (its a chain department store). While walking you will go up a flight of stairs and back down, continue walking, the underground station will split into four walking lanes, each lane is lined with stores. Pick the 3rd lane from the left. Continue walking until you reach Diamond exit 北 8 or 9 (either one). Go up the stairs on the the left to the outside. Continue walking after only a few yards you will reach a river, if you don't you went the wrong way and turnaround. Continue past the river and you will meet an intersection that can be crossed by overhead pedestrian bridges. Look to your right and Sansui will be there.
Getting to the Shibuya store, get off Shibuya station (there are two stations so it can be confusing, get off the one with the famous dog statue). I'm not sure which exit it is but if you get out and enter the square with the famous dog statue you're at the wrong spot. Go back through the station to the opposite side. Outside there will be a bus stop area, go right and you will reach a pedestrian bridge walk up and then down (still going right). One you walk down the bridge, Sansui is not far from there to your right. I believe the street is Meiji Dori.
If you in the Square with this dog statue, head back through the station to the other side.
Ikebukuro store took me forever to find but I finally found it just when I was about to give up on it. Get off the Ikebukuro station take the east exit. Once outside turn left, you'll past a Parco Department Store (at least you did in 2010). You'll hit a stoplight. Turn left and follow the street, it will diagonal abit. Follow it to the wall the blocks you from the railroad. Turn up and start walking. To your left will be a small park and Sansui will be on the right.
If you you see this you're heading the right direction.
Sansui Ikebukro store.
I forgot to take pictures of the other two.
Another store that I did not make it to on this trip is the A&F Country store in Ginza . This store is located (at least it was back in 2004) in the Matsuzakaya Department store in Ginza. It is located on B2 level. I found this store by accident in 2000, I was heading to the tax refund area and ran into this shop. A&F is similar to what REI is here, outdoor gear but this store had a fly fishing section. It was at least back in 2004 pretty well stocked. Unlike the Sansui stores this store (I believe) allows you to get tax refund for foreigners because it is in a department store if you spend over ¥10,000 (or something like that amount) which is roughly $100US. UPDATE 6.19.12 My Japanese friend Koji has let me know that A&F is no longer so don't waste your time going to find it. What a shame.
If your are fortunate to read Japanese, here are the two stores websites.