Recording the King of Instruments well is always a challenge but, when well done, it can be extremely rewarding.
This is a complex subject, thus only the most general information and pros and cons as it relates to nice sound are described here:
When contemplating the type and arrangement of microphones used to undertake such a task, one needs to bear in mind that no two pipe organs, even from the same builder, are ever exactly the same, and certainly no two halls, auditoriums, theatres, chapels, abbeys, churches, cathedrals, or residences are the same, so no exact information can be offered in that respect; in each unique situation it really is a case of experimentation and using the ear.
Since one would want a stereo recording in this case, the use of a spaced pair of A/B omni's (omni-directional microphones) are usually the first choice for the main pickup (photo).
Omni-directional microphones are microphones that pick up sound with equal gain from all sides or directions of the mic; this means that whether an organ pipe speaks into the mic from the front, back, overhead, left or right side, it will record the signals all with equal gain; this is very useful when the sound needs to be recorded from multiple directions, as when organ pipes are positioned in different locations within the room.
Big pipe organs are among the few instruments with a real low end worth capturing; for recording any organ which can sound 16-foot stops on low C, the sensitivity of the mics used should be able to capture frequencies at least down to 32Hz; for capturing sounds in the 32-foot octave, one would try to use a mic with a sensitivity down to as close to 16Hz as possible to minimize any non-musical ambient rumble; this will be possible because certain mics (albeit the most expensive ones) are sensitive down to 5Hz.
Tall mic stands can be helpful when recording a pipe organ, but since professional builders and voicers make their final voicings to sound good from pews/seats, not 20 or 30 feet up in the air, such stands should be positioned to pick up the signal in the room from where people are seated.
While finish voicers "tune" the organ for what it sounds like down at the listener level in the installed space, it's also the case that the best omni-mics don't hear sound with quite the same complex directional sensitivity that our brain-ear-pinna system does; we often "cheat" the mic much higher than listener level because it "creates" the same sound (as heard by the mic) that we hear with our ears down on the ground -- an added benefit being that getting the mics higher off the ground puts more space between the mics and any audience noise that may occur in a live recording.
These omni-mics would need to be positioned far enough away from the pipes that they take in the acoustics; the room is the dictating factor here; one should NEVER close-mic the organ, as it's not voiced to be heard from right up on the facade or from right in front of the tone grilles.
The capture of the room's ambience is ABSOLUTELY necessary for bringing the sound of the instrument together.
Beyond that there is no formula for mic placement, only good judgment by LISTENING on site for both clarity and room capture; the idea with mic placement is to arrive at a good balance between direct sound from the organ and natural reverb from the building.
The term Critical Distance describes the point, measured from the sound source, at which the direct signal and the reflected or reverberant signal are of equal intensity.
To find this Critical Distance requires a long tape measure, a sound level meter, and some means of generating a reasonably constant level of sound in the room which, in this case, should come from the area where the pipes are located.
One would start by measuring the noise level of the sound source at close range and making a note of the reading; this distance is then doubled and measured again; the noise level will have reduced by a certain amount because one would be in the direct field where a doubling of distance results in a halving of level.
One would then keep doubling the distance and measuring the drop in level from the previous position; while one is in the direct field, each doubling of distance results in a level drop, but as one nears the point where the direct and reverberant fields are equal in level, the level drop will get much smaller.
A change of only a decibel or two indicates that the Critical Distance has been found; further increases in distance will result in no significant change in level at all, because one is now in the reverberant field.
In general, organ lofts and pipework are built fairly high, and so a very tall mic stand or boom helps to get the mic(s) more on axis to the pipework; it's then a case of moving the mic around to get the best balance between the different divisions or sections.
If the organ is large and the pipework is installed in multiple locations, it may be necessary to use several mics to cover everything to attain the best balance; in the case of a pipe organ one may well be able to achieve an acceptable stereo effect using separate, panned, mono mics instead of (or in addition to) a stereo pair.
This is important because as one moves away from the pipes, the closer the mics are placed to the Critical Distance, the more reverberation will be picked up, and moving the mics closer to the source will result in a drier sound.
Recording engineers tend to go for a main stereo pair of mics to give the best overall balance and acoustic impression of the room, and then add additional (usually) mono mics if needed to reinforce a particular section or type of sound just to provide a little extra clarity or definition.
While the premise may be good, with pipe organs these additional mono mics, by giving certain sounds or voices a boost, will change what the listener actually hears from the instrument on site.
In an interestingly dry space where the reverberation may be less than one second, it's tough on the organist who has to adjust many things (touch, tempo, values of chords and intervening rests, possible release of final chords, etc.) to get the music to "sound"; it could mean abandoning for the time being the entire system of touch under which that organist was trained; the performer is faced with changing the score mentally to make the music the composer wrote on the page to come across; it's also tough to figure the Critical Distance for mic placement because the reverberation field is so small relative to the direct field.
The room is very much the "sound board" of a big pipe organ, thus the organist plays the room right along with the instrument; any time the acoustics are sufficiently dry like this, one would want all the hall one could get on the recording; sometimes a smaller spacing between mics improves the stereo picture a bit, but one would have to listen to know for sure; one might also experiment with an even more distant spacing from the chamber grille just to generate as much ambient reverb as possible.