Note: Most of this came from Wikipedia.org
keyboard = manual

Stops:
Controls at the console called stops select which ranks of pipes are used.   These controls are generally either draw knobs (or stop knobs), which engage the stops when pulled out from the console; stop tablets (or tilting tablets) which are hinged at their far end; or rocker-tablets, which rock up and down on a central axle.   Different combinations of stops change the timbre of the instrument considerably.   The selection of stops is called the registration.   On modern organs, the registration can be changed instantaneously with the aid of a combination action, usually featuring pistons.   Pistons are buttons that can be pressed by the organist to change registrations; they are generally found between the manuals or above the pedalboard. In the latter case they are called toe studs or toe pistons (as opposed to thumb pistons).   Most large organs have both preset and programmable pistons, with some of the couplers repeated for convenience as pistons and toe studs.   Programmable pistons allow comprehensive control over changes in registration.   Newer organs may have multiple levels of solid-state memory, allowing each piston to be programmed more than once.   This allows more than one organist to store their own registrations.   Many newer consoles also feature MIDI, which allows the organist to record performances.   It also allows an external keyboard to be plugged in, which assists in tuning and maintenance.  
The stops controlling each division (see Keyboards) are grouped together.   Within these, the standard arrangement is for the lowest sounding stops (32´ or 16´ to be placed at the bottom of the columns, with the higher pitched stops placed above this, (8´ 4´ 2 2/3´ 2´ etc.); the mixtures are placed above this (II, III, V, etc.).   The stops controlling the reed ranks are placed collectively above these in the same order as above, often with the stop engraving in red.   In a horizontal row of stop tabs, a similar arrangement would be applied left to right rather than bottom to top.   Among stops of the same pitch, louder stops are generally placed below softer ones (so an Open Diapason would be place towards the bottom and a Dulciana towards the top), but this is less predictable since it depends on the exact stops available and the space available to arrange stop knobs.    

For Instance: tab colors for the New Palace Theatre Organ:

4´ Clarion
16´ Trombone	8´ Trumpet
2´ Fifteenth	V Mixture
4´ Principal	2-2/3´ Twelfth
8´ Dulciana	4´ Harmonic Flute
8´ Open Diapason	8´ Stopped Diapason
16´ Double Open Diapason
Gt Super Octave	Gt Sub Octave
Swell to Great	Choir to Great

From the following it will be seen that anything that switches something off is red, whether a cancel piston, a coupler, or a 'mute' of some type.   Celeste stops, which are next to their unison stop, are also engraved red to distinguish them from their 'in tune' partner.  
The final colour coding for the stop tabs is -

Tonality	Tab Colour	Engraving colour
Diapason	Off White	Black
Diapason Celeste	Off White	Red
Open Flute	Ivory	Black
Stopped Flute	Ivory	Brown
Flute Celeste	Ivory	Red
String	Blue	White
String Celeste	Blue	Red
Tibia	Grey	White
Chorus Reeds	Black	White
Orchestral Reeds	Red	White
Tonal Percussion	'Moddled' Yellow	Black
Atonal Traps	'Moddled Yellow	Red (originally White)
Midi & Electrophone	Green	White

The illuminated 'Touch Stops' are colour coded as follows -

Function	Stop Colour	Engraving colour
Octave & Sub-octave Couplers	Blue	White
Unison Coupler	White	Black
Unison Off	Red	White
Pizzicato Coupler	Yellow	Black
Harmonic Coupler	Yellow	Black
Division Transfer	Green	White
Mute	Red	White

Although not standard by any means, the thumb pistons are also coloured, as follows -
Cancel pistons are Red
Reversible pistons are Green
Divisional and General pistons are Yellow
The Memory Set piston is White

Thus, an example stop configuration for a Great division may look like this:

4´ Clarion
16´ Trombone	8´ Trumpet
2´ Fifteenth	V Mixture
4´ Principal	2 2/3´ Twelfth
8´ Dulciana	4´ Harmonic Flute
8´ Open Diapason	8´ Stopped Diapason
16´ Double Open Diapason
Gt Super Octave	Gt Sub Octave
Swell to Great	Choir to Great

The standard position for these columns of stops (assuming drawknobs are used) is for the Choir or Positive division to be on the outside of the player's right, with the Great nearer the center of the console and the music rest.   On the left hand side, the Pedal division is on the outside, with the Swell to the inside.   Other divisions can be placed on either side, depending on the amount of space available.   Manual couplers and octave extensions are placed either within the stop knobs of the divisions that they control, or grouped together above the uppermost manual.   The pistons, if present, are placed directly under the manual they control.  

Manuals:
Collection of ranks controlled by a particular manual is called a division.
Names of divisions: Great, Swell, Choir, Solo, Orchestral, Echo, Antiphonal
"Choir" is a corruption of "Chair", as this division initially came from the practice of placing a smaller, self-contained, organ at the rear of the organist's bench.[dubious – discuss] This is also why it is called a Positif which means portable organ.



Main manual = Great

	2 Manual	3 Manual:	4 Manual:	5 Manual:
V				Echo
IV			Solo	Solo
III		Swell	Swell	Swell
II	Swell	Great	Great	Great
I	Great	Choir	Choir	Choir

Divisions not assigned to a manual: Floating
        Played by coupling to another manual
Temperamant: organ tuning system
Modern organs are typically tuned in equal temperament, in which every semitone is 100 cents wide.   Many organs that are built today following historical models are still tuned to historically-appropriate temperaments.
Cent is a logarithmic unit of measure used for musical intervals.   Twelve-tone equal temperament divides the octave into 12 semitones of 100 cents each.   Typically, cents are used to express small intervals, or to compare the sizes of comparable intervals in different tuning systems, and in fact the interval of one cent is too small to be perceived between successive notes.  


One cent compared to a semitone on a truncated monochord.


Octaves increase exponentially when measured on a linear frequency scale (Hz).


Octaves are equally spaced when measured on a logarithmic scale (cents).

Interval is a frequency difference (I think).

The range (compass) of the keyboards on an organ has varied widely between different time periods and different nationalities.   Portative organs may have a range of only an octave or two.   The modern console specification recommended by the American Guild of Organists calls for manual keyboards with sixty-one notes (five octaves, from C to c´´´´ and pedal keyboards with thirty-two notes (two and a half octaves, from C to g´   These ranges apply to the notes written on the page; depending on the registration, the actual range of the instrument may be much greater.  

Enclosure and expression pedals
On most organs, at least one division will be enclosed.   On a two-manual (Great and Swell) organ, this will be the Swell division (from whence the name comes); on larger organs often part, or all of, the Choir and Solo divisions will be enclosed as well.  
Enclosure is the term for the device that allows volume control (crescendo and diminuendo) for a manual without the addition or subtraction of stops.   All the pipes for the division are surrounded by a box-like structure (often simply called the swell box).   One side of the box, usually that facing the console or the listener, will be constructed from vertical or horizontal palettes (wooden flaps) which can be opened or closed from the console.   This works in a similar fashion to a Venetian blind.   When the box is 'open' it allows more sound to be heard than if it were ´closed´.