Well I have to be honest that this report is not really about watch shopping in Tokyo as I did not really take photographs or take down notes. However if you are in Tokyo and want to have a view of what watches are available here in Tokyo, there are a number of places you can go.
I 'checked' out two of the department stores in Ginza and can say that the selection and brands are just awesome. Check out Mitsukoshi and Matsuya. The brands represented there is vast, as is the selection within each brands. You can also find limited edition watches for the Japanese markets at these department stores.
Another place I went and had a quick view of what they had was Aqua City at Odaiba. Here you can find the Casio G-Shock factory (I am sure one of many all over Tokyo). They too have many watches that are 'just' for the Japanese market. In this mall you will also find Swatch and if you are into collaboration watches, there is Stussy.
In the Shinjuku area there is Isetan. The watch brands represented here is even bigger as compared to Mitsukoshi (Ginza). The selection of Panerai watches here is just awesome. I found watches from the 2009 and 2010 limited edition collection here. You can also find 'boutique' only watches (well in AP Taiwan anyway) here in Isetan. Again if you are into collaboration watches, you can find watches by United Arrows (where I got my Benrus) and Beams.
Again this is not a really comprehensive report but I can say that there are many many shops here in Tokyo selling both new and pre-loved watches. Oh before I forget, some stores do offer the Tax refund thing but not all. So ask and check if they do.