Giga Studio
I have tried this venerable program and found it difficult to use with organs, since predefined combinations needed to be used instead of just adding stops. Also, it is disk-based and looping is optional, so it was possible to run out of sound for organ points. It may be substantially improved now.

Hauptwerk
This “Virtual Pipe Organ Project” has been my most prolific interface so far, accounting for 2318 tracks (368 tracks using HW2 or HW3=21.50 hours, 1950 tracks using HW1=121.85 hours). There are now 1179 unique tracks in my collection, so most tracks are realized on at least two instruments, but with varying degrees of enhancement depending on age of track and instrument characteristics.

MyOrgan
If not prohibited by the sample vendor, owners of Hauptwerk 1 samples can gain a little more efficient use of their current hardware resources by using this controversial but free interface. A little demonstration of MyOrgan features is available here. Various demos can be found here. The wet tracks I've made using St. George's Casavant, Op. 2871 and A French Harpsichord after Blanchett have been integrated into Virtually Baroque: 99 tracks, for a total of 8.62 hours of music.

SOUND FONTS
Can a SoundFont Change One's Life?
The JEUX SoundFont just about did that for me. Download Version 1.4 and many other sampled sounds at HammerSound SoundFont Library. There are several midi files you can play at John McCoy's website. If interested in exploring temperaments with SoundFonts, try the Java Microtuning Organ.

jOrgan
The Marcussen and the "new" Steevens/Van Assendelft samples have been made available in SoundFont format designed for this freeware.

OTHER RESOURCES
midiorgan.com is a tremendous resource for MIDI and sampled organ enthusiasts, though right now it is a bit out of date. The webmaster has programmed random organ photographs to appear on the first page - just hit reset or refresh on your browser.

NEW FRONTIERS
Someone is probably working on a wonderful, user-friendly and highly efficient new interface. If you have anything to add to my knowledge, please email me at jocr@toast.net.