During both the books and the movies we see glimpses of the Ministry of Magic. Did they include all of the features at each level of the elevator? We know for example that the Department of Mysteries is on the same level as the courtrooms for the Wizengamot. What else do the books/movies plus sites such as Pottermore and JKR's personal interviews tell us about the organization of the Ministry of Magic?
To get between the different levels at the Ministry, you have to use a lift. The Ministry have been kind enough to equip the lift with a disembodied voice which describes every level – helpful for a lost traveller, or somebody describing the Ministry for a post on the Internet. Both use cases I’m sure the original designers had in mind.
Between two of Harry's trips to the Ministry – for his hearing in Order of the Phoenix, and breaking in to steal the locket in Deathly Hallows – he’s been to every floor visited by the lift. Below are the descriptions from each level.
(I don’t think we get discussion of Ministry HQ in other media – e.g. Pottermore or interviews – but we don’t really need it.)
Higher numbers are further underground.
“Level one, Minister of Magic and Support Staff.” [DH]
“Level two, Department of Magical Law Enforcement, including the Improper Use of Magic Office, Auror Headquarters, and Wizengamot Administration Services.” [OotP]
“Level three, Department of Magical Accidents and Catastrophes, including the Accidental Magic Reversal Squad, Obliviator Headquarters, and Muggle-Worthy Excuse Committee.” [OotP]
“Level four, Department for the Regulation and Control of Magical Creatures, incorporating Beast, Being, and Spirit Divisions, Goblin Liaison Office, and Pest Advisory Bureau.” [OotP]
“Level five, Department of International Magical Cooperation, incorporating the International Magical Trading Standards Body, the International Magical Office of Law, and the International Confederation of Wizards, British Seats.” [OotP]
“Level six, Department of Magical Transport, incorporating the Floo Network Authority, Broom Regulatory Control, Portkey Office, and Apparation Test Center.” [OotP]
“Level seven, Department of Magical Games and Sports, incorporating the British and Irish Quidditch League Headquarters, Official Gobstones Club, and Ludicrous Patents Office.” [OotP]
“Level eight,” said the witch’s cool voice, “Atrium.” [DH]
When the time and place of Harry’s hearing is changed, we find out that the Department of Mysteries occupies level nine:
The lift clattered into view and they hurried inside. Every time it stopped Mr. Weasley cursed furiously and pummelled the number nine button. […]
“Department of Mysteries,” said the cool female voice, and left it at that. “Quick, Harry,” said Mr. Weasley as the lift doors rattled open, and they sped up a corridor that was quite different from those above.
When they’re going to the courtroom, we learn that there are levels even deeper in the Ministry:
Mr. Weasley seized him by the arm and dragged him to the left, where there was an opening leading to a flight of steps.
“Down here, down here,” panted Mr. Weasley, taking two steps at a time. “The lift doesn’t even come down this far… why they’re doing it there…”
But we don’t find out anything beyond courtrooms and the Department of Mysteries.
HP Lexicon tells us that there are ten levels to the Ministry of Magic, not counting the phone-box visitors' entrances. @alexwlchan has already given descriptions of each level in his excellent answer, but I can do more than just descriptions...
Level 1: the offices of the Minister for Magic and administrative staff.
Level 2: Department of Magical Law Enforcement.
Level 3: Department of Magical Accidents and Catastrophes.
- Accidental Magic Reversal Squad
- Obliviator Headquarters
- Muggle-Worthy Excuse Committee
Level 4: Department for the Regulation and Control of Magical Creatures.
- Beast, Being, and Spirit Divisions
- Goblin Liaison Office
- Pest Advisory Board
Level 5: Department of International Magical Cooperation.
- International Confederation of Wizards, British Seats
- International Magical Office of Law
- International Magical Trading Standards Body
Level 6: Department of Magical Transportation.
- Apparition Test Center
- Broom Regulatory Control
- Floo Network Authority
- Portkey Office
Level 7: Department of Magical Games and Sports.
- British and Irish Quidditch League Headquarters
- Official Gobstones Club
- Ludicrous Patents Office
Level 8: Atrium.
Level 9: Department of Mysteries.
Level 10: Courtroom Ten.
(all maps and descriptions sourced to HP Lexicon)