Dalek hierarchy

Due to their highly militaristic culture, the Daleks operated under what was nominally a rigid hierarchy. Its exact structure was highly variable over time, however.

Figurehead
The Daleks were typically led by the Dalek Emperor (TV: The Evil of the Daleks, The Parting of the Ways); the overall leader of the Dalek Empire and Skaro. However, this was not always the case; during the Imperial-Renegade Dalek Civil War, Davros, the creator of the Daleks, was installed as Emperor of the Imperial Daleks. (TV: Remembrance of the Daleks)

Also, in an alternate timeline, the Daleks were led by the Mentor, the creator and leader of a faction of Daleks from that universe. (AUDIO: Dalek War: Chapter One)

Usually ranking beneath the Dalek Emperor was the Dalek Supreme--high-ranking generals, commanding major operations or planetary occupations. However, in the absence of a Dalek Emperor, Dalek Supremes would often take command. In the early days of the Daleks, the Supreme was the direct second-in-command to the Emperor. (COMIC: The Dalek Chronicles) However, during the Imperial-Renegade Dalek Civil War, the Renegade Dalek faction was led by a Supreme instead of an Emperor. (TV: Revelation of the Daleks) In the New Dalek Empire, a Red Supreme Dalek took command. (TV: The Stolen Earth)

In the creation of the New Dalek Paradigm, the Dalek race was reorganised into a colour-coded caste society; the leader of this first batch of Daleks was the white Supreme Dalek. (TV: Victory of the Daleks) Later, two New Paradigm Dalek Emperors were encountered by the Doctor; one blue, and the other purple. (GAME: City of the Daleks, The Eternity Clock) Eventually, the Parliament of the Daleks was created, led by the Dalek Prime Minister. This Dalek took the place of the standard Dalek Emperor, and outranked the New Paradigm Supreme Dalek. (TV: Asylum of the Daleks)

There also existed the Dalek time controller, which was given strategic command over all Dalek missions involving time travel. (AUDIO: Patient Zero) At one point, the Dalek time controller assisted the New Dalek Paradigm and outranked even the Supreme Dalek in certain cases. (PROSE: The Dalek Generation)

Council
The Cult of Skaro was a council of elite Daleks created to think of imaginative strategies, previous to or during the Last Great Time War. (TV: Doomsday)

The Dalek Council was a governing body under the Emperor. (REF: Doctor Who: Aliens and Enemies) In some instances, they appeared to rule the Daleks in the permanent or temporary absence of an Emperor. (TV: The Daleks, Planet of the Daleks)

The Emperor had a squad of black-domed Daleks as his personal guard that were usually seen protecting and serving it. (TV: The Evil of the Daleks) Some versions were equipped with two gunsticks. (TV: The Parting of the Ways)

A large convocation of New Paradigm Daleks, led by the Supreme Dalek and the Dalek Prime Minister was known as the Parliament of the Daleks. (TV: Asylum of the Daleks)

Commanders

 * Dalek Supreme - White New Paradigm Dalek seen in Victory of the Daleks
 * Dalek Supreme Controller - Black Daleks during the 22nd century Dalek invasion, later Red Daleks, second to the Supreme. (AUDIO: "Death to the Daleks!")
 * Dalek Inquisitor General - the Supreme Dalek's Inquisitor General during the Second Dalek War. Dalek X was the best known, if not the only, example (PROSE: Prisoner of the Daleks)
 * Dalek Scientific Division - high-ranking, their needs overrode all other orders and concerns in at least one mission (AUDIO: Return of the Daleks). Science Daleks were claimed to be silver (The Dalek Tapes). It was also shown that the Eighth Doctor met a green Dalek scientist. The Scientist Daleks of the New Dalek Paradigm are ranked by their orange colour scheme. (TV: Victory of the Daleks)
 * Strategist Dalek - Blue New Paradigm Dalek (TV: Victory of the Daleks)
 * Eternal Dalek - Yellow New Paradigm Dalek (TV: Victory of the Daleks)
 * Dalek Saucer Commander
 * Red Dalek
 * Blue Dalek - equivalent of non-commissioned officers (PROSE: War of the Daleks)

Low Ranking Daleks

 * Astrodalek
 * Dalek drone - also known as the Drone Dalek - the basic drones were bronze, while their superiors were larger and red in colour.
 * Special Weapons Dalek - designed solely for combat, lacking the abilities of the standard Dalek.
 * Marsh Dalek - designed solely for swamp combat.
 * Spider Dalek
 * Marine Dalek
 * Human-Daleks - humans altered with the Dalek Factor or Dalek DNA.
 * Dalek puppet - Other beings that have been converted into partial Daleks by the nanocloud.

Non-Daleks servants and slaves
Several non-Dalek species worked under the Daleks under some form of enslavement.

Robomen were slaves under heavy mind control, (TV: The Dalek Invasion of Earth) while Dalek Troopers worked as mercenaries. (TV: Resurrection of the Daleks)

A robotic duplicate of the First Doctor was sent to kill the original. (TV: The Chase)

According to one account, the Movellans were servants to the Daleks, the war against them having been hoaxed. (PROSE: War of the Daleks)

The Mighty Jagrafess of the Holy Hadrojassic Maxarodenfoe were part of the Daleks' plan to alter the minds of the Fourth Great and Bountiful Human Empire, (TV: The Long Game, Bad Wolf) and was the master of the the Editor of Satellite Five, and by extension, the entire Empire. (TV: The Long Game)

Other enslaved species included the Exxilons (TV: Death to the Daleks) and the pig slaves. (TV: Daleks in Manhattan / Evolution of the Daleks)

Mercenaries
Ogrons were mercenaries of the Daleks, (TV: Day of the Daleks) as were Werelox. (COMIC: Doctor Who and the Dogs of Doom)

Visual distinctions
Daleks often showed their rank via colours. In one version, gold Daleks were the highest, followed by black, red, blue, and grey. (PROSE: War of the Daleks)

In the early days, the majority of Daleks were silvery with blue "bumps", with mid-ranking Daleks like the Saucer Commanders being partially black and a black Dalek Supreme as the highest commander. (TV: The Dalek Invasion of Earth)

During the Last Great Time War and in the New Dalek Empire, almost the entirety of Daleks shown were of the same colour; the Supreme Dalek in the latter was marked out by being red with golden trimmings, while Dalek Sec of the Cult of Skaro was black.

The restored Daleks sported bright colours, with each colouring showing their role: the Supreme was white, the strategist was blue, the scientist was orange, and the drones were red. The yellow Dalek was given the mysterious title of "Eternal" and was the only one to have black orbs instead of silver. (TV: Victory of the Daleks, Doctor Who Confidential)

Purity
Daleks ranks were often established by their genetic purity. In Parting of the Ways, the Dalek Emperor created his new army out of human DNA, which caused them to not only obey but worship the Emperor as the only pure Dalek.

Davros later rebuilt the Daleks species from his own cells and used them to create the New Dalek Empire. The leader was a Supreme Dalek with a unique red and gold casing. However, Davros and Caan were not allowed to lead, as the Daleks saw them both as impure. (TV: The Stolen Earth/Journey's End)

When the new Dalek Race was created from pure Dalek DNA found in the progenitor both they and the impure Daleks which created them believed the new race was superior due to their purity, and that any impure forms must be destroyed. (TV: Victory of the Daleks)

History
The original Dalek hierarchy saw the Dalek Emperor as the overall leader of the Daleks. Daleks with black domes acted as both the Emperor's guards and lieutenants. (TV: The Evil of the Daleks) Black Daleks acted as Supreme Controllers during planetary invasions and other missions of high importance, and were part of a tier of Dalek commanders. (REF: Doctor Who: The Dalek Handbook) Each Dalek saucer was put under the command of a Dalek Saucer Commander. (TV: The Dalek Invasion of Earth) Dalek drones had silver casing.

This hierarchy for the most part remained unchanged until the defeat of the humanised Daleks at the end of the Great Civil War, after which the Daleks were able to restore order and rebuilt. A new hierarchy was established. The Dalek Emperor remained the overall ruler, but black Supreme Daleks were replaced with gold Daleks (TV: Day of the Daleks, Frontier in Space) and Dalek workers and soldiers were distinguished by their grey casings. (REF: Doctor Who: The Dalek Handbook) A Dalek Council was also organised, of which a special black and gold Dalek was a member among others. (TV: Planet of the Daleks) Dalek taskforces were silver with black globes. (TV: Death to the Daleks)

After the Time Lords sent the Fourth Doctor on a mission to prevent the creation of the Daleks, some points of Dalek history were supposedly changed. Grey Daleks remained as drones and took orders from the Supreme Dalek, a position which black Daleks once again took up rather than gold. This was an unstable arrangement, as discovered during the Dalek-Movellan War. With both the Daleks and the Movellans at a logical stalemate, the Daleks went in search of Davros to gain his aid in resolving the situation. (TV: Destiny of the Daleks) Davros was displeased to learn that the Daleks were taking orders from a Supreme Dalek instead of him. He built his own Daleks to oppose those of the Supreme Dalek and declared himself the Dalek Emperor. A civil war between Davros' white and gold Imperial Daleks and the "Renegade Daleks" loyal to the Supreme Dalek broke out. Neither side could claim victory. (TV: Resurrection of the Daleks, Revelation of the Daleks, Remembrance of the Daleks)

During the Last Great Time War, Dalek soldiers had bronze casings and were led once again by the Emperor. Davros also took part in the war but was supposedly killed during the first year. (TV: The Stolen Earth) Following the near-destruction of both the Time Lords and the Daleks, what Daleks managed to survive attempted to rebuild their race. The Cult of Skaro - a secret Dalek order - tried twice but were foiled by the Doctor on both occasions. The Cult's leader, Dalek Sec, had a completely black casing while the other three - Thay, Jast and Caan - had the standard bronze, although they were more than just soldiers. In the end, Sec was overthrown and Caan replaced him. (TV: Doomsday, Daleks in Manhattan/Evolution of the Daleks)

Caan, the last of the Cult, escaped from the Doctor back into the Time War, where he rescued Davros but lost his sanity due to breaking the time lock. Davros rebuilt the Daleks from his own cells and created the New Dalek Empire. The leader was a Supreme Dalek with a unique red and gold casing. Davros and Caan were not allowed to lead, as the Daleks saw them both as impure, demonstarting how strict the Daleks were about purity in their race and leadership. The Empire was obilterated by a clone of the Tenth Doctor. (TV: The Stolen Earth/Journey's End)

The Dalek race was finally restored fully after the only survivors of the New Dalek Empire's destruction came across a Progenitor device. The restored Dalek race was led by a white Supreme Dalek. Drone Daleks were red, strategists were blue, scientists were orange, and the Eternal Dalek was yellow. (TV: Victory of the Daleks) These Daleks also had an Emperor which was blue, but when the Eleventh Doctor prevented the Daleks from taking control of Skaro, no Dalek became the Emperor and so the Supreme Dalek likely continued to lead the Daleks full time. (GAME: City of the Daleks)

Behind the scenes
The Dalek Tapes, a feature in the Genesis of the Daleks DVD, has golden Daleks as members of the Supreme Council, followed in rank by black (Dalek Supreme), partially black, silver (scientific corps), and grey. Doctor Who: The Dalek Handbook states that the Black Daleks used to be the highest command until the civil war, and a Supreme was always taken from their ranks; after the war, the Supremes and their Council were gold-and-black, the Black tier was replaced with the golden Commanders, and the standard Daleks were grey-black, with a group commander picked from their ranks.