Some still surviving organs that Bach had played off of my head:
Hamburg Jacobi
Hamburg Katharenkirche (Reconstituted by Flentrop recently)
Trost in Altenberg
Trost in Walterhausen (OAM sample, but no actual records show that Bach played the organ. It's very possible, though, that he did test out the organ, as it was essentially Trost's Magnum opus.)
Weißenfels Schloss organ (Can't find further info on it)
Sonnenorgel (Sampled by SP, but only a few pipes are incorporated in a Romati-roque organ)
Arnstadt Bach-kirche (Also only a few pipes)
Luneburg Johanniskirche (The rennaisance organ that Bach played was converted, however, into a full-blown Baroque organ a few years after Bach left his lessons with Bohm, the organist)
Merseburg dom (quite a few stops incorporated in a spectacular and famous Romantic organ that Liszt later played)
Störmthal
Schlosskirche Harbke
Zschortau
Also possible:
Grasberg Schnitger
Cappel Schnitger (captured in a rather old sampleset)
Lubeck Jacobikirche's 2 organs - Buxtehude probably also walked down the street from the Marienkirche and played these too
The small positiv in Halle's Marktkirche
Out of these, the only ones I would particularly like to own a sample of are the first two and last two(But of course, for now these are rather extravagant pipedreams
) - you can probably see that my Bach organs of choice are huge Northern German ones, historically accurate or not.
Pardon this long post. I just like making lists
Edit: oops; I forgot the obvious one in Naumburg.