Based on MRed94's downloadable Excel spreadsheet version, here is a web-based list of all the hotkeys you can use in Pharaoh.

A Orders a selected warship to attack all enemies.
C Shows the Risks: Crime Overlay
C Orders a selected charioteer company to charge.
D Shows the Risks: Damage Overlay
E Orders a selected transport ship to evade enemies.
F Shows the Risks: Fire Overlay
F Orders a selected company to return to its Fort.
H Orders a selected ship to hold its current position.
L Centers your view on a different military company each time it is pressed.
L Orders a selected company to hold ground in Loose Formation.
M Monument selected, shows how much land the monument will occupy. Pressing M freezes the monument's footprint into place so that you can move around the city without moving the monument's tentative location. Press M again to resume normal mouse behaviour.
M Orders a military company to commence "mop-up" behaviour.
N Orders a selected company or warship to attack nearby enemies.
P Pause
R Rotates statues, gatehouses, or temple complexes 1/4 turn. Statues will display multiple styles.
R Orders a selected company to rotate their position.
R Orders a selected ship to return to the Shipwright for repairs.
T Shows the Risks: Problems Overlay
T Orders a selected company to "hold ground in tight formation."
W Shows the Water Overlay.
W Orders a selected ship to return to its home Wharf.
SPACE Toggles between your last selected overlay and the normal city view.
ESC Exits the game.
[ Reduces game speed by 10 percent.
] Increases game speed by 10 percent.
Apostrophe Overseer of the Workers.
1 Overseer of the Military.
2 Political Overseer.
3 Ratings Overseer.
4 Overseer of Commerce
5 Overseer of the Granaries
6 Overseer of Public Health
7 Overseer of Learning
8 Overseer of Diversions
9 Overseer of the Temples
0 Overseer of the Treasury
minus sign Chief Overseer
equals sign Overseer of Monuments
F7 Sets 640 x 480 screen resolution
F8 Sets 800 x 600 screen resolution
F9 Sets 1024 x 768 screen resolution