Hey,
Below are a couple of PDFs. The first one I scanned right out of an old pipe organ method book. It has lots of facts on the history of organs, and even goes through the different stops and how to use it's different registrations.
The other PDF, I found somewhere on the internet, I forget where. But it covers organ registration a little bit more.
Also, the 3rd link is goes to a website of an Encyclopedia of Organ Stops. It gives descriptions of all kinds of stops, some even have sound clips. This is a great website to use side-by-side with the first PDF provided.
I hope this helps. It helped me a lot.
Enjoy!
-Geremie
http://f1.grp.yahoofs.com/v1/EO_USZMtrNg85SiFAu8VBw481wboMRav7EDPhbukk_XuAKC6DUq4nMfySe1M3wZwf3J3gU70HoOtoBuhd2wfVA/Pipe%20Organ%20-%20History%20and%20Intro.pdf
http://f1.grp.yahoofs.com/v1/EO_USWZT3gc85SiFmIbo4a-0Ms7-Uo0mXwHmc-0bMeTnzkC5UTd7u9uoX-jIXS-V2D3spo-wmHldlDR4oIszow/Organ%20Registration.pdf
Encyclopedia of Organ Stops
