In previous posts at the Seforim blog, we have attempted to highlight some of the more recently printed books, which are fairly easy to come by. However, I thought it worthwhile to mention some slightly older books, which are generally more difficult to obtain and where they can be obtained. I will highlight the contents of one store -- Moznaim (718-438-7680) -- in Boro Park.
First, for literature of the Geonim, they have the Teshuvot HaGeonim. In this set, the majority of volumes are fairly easy to get, but there are two volumes which are less common - Ginzei Schechter and Louis Ginzburg's Geonica. Both of these are available from Moznaim.
Second, the four volume Auerbach's edition of R. Avraham b. Azriel's Arugat HaBosem, which is a key work on piyut/siddur, is available there as well.
Third, Mordecai Wilensky's Hasidim u-Mitnagdim collects the various early polemics for and against the Hassidic movement, is available in two-volume paperback.
Aside from the Geonim, Moznaim also has an extensive selection of Midrashim - most of the time the most important critical edition of a particular Midrash.
Finally, although not out-of-print or the like, Moznaim also has redone the Mishnayot for Seder Zeraim and Teharot. These include the standard commentaries (e.g. Ra"SH and Rambam) and some other less common ones all with a nice layout. Additionally, they have made corrections based upon manuscript data and the older version of the text is available in footnote form.
These are a sampling of a few which I came across, I am sure there are many more hidden gems to unearth.