General Shortcuts:

Ctrl + N : New Project
Ctrl + O : Open Project
Ctrl + S : Save Project
Ctrl + Shift + S : Save Project As
Ctrl + Z : Undo
Ctrl + Shift + Z : Redo
Ctrl + Shift + D : Duplicate Layer
Ctrl + Shift + C : Copy Layer
Ctrl + Shift + V : Paste Layer
Ctrl + A : Select All
Ctrl + D : Deselect All
Ctrl + Shift + F : Frame Selection
Delete : Delete Selected Items
Spacebar : Temporarily switch to the Pan tool
Ctrl + Spacebar : Temporarily switch to the Zoom tool

Viewport Navigation:

Alt + Left-click : Rotate View
Alt + Middle-click : Pan View
Alt + Right-click or Scroll : Zoom In/Out
Ctrl + Shift + Left-click : Focus on an object in the 3D view
F : Frame Selected Objects
Shift + Z : Fit to Screen

Painting and Texturing:

B : Brush tool
E : Eraser tool
C : Clone tool
X : Eyedropper tool (Picks color and material)
F : Fill tool (Bucket)
Shift + F : Flood Fill tool
W : Wand Selection tool (Magic Wand for selecting areas)
Ctrl + G : Group Selected Layers
Ctrl + Shift + G : Ungroup Selected Layers
G : Toggle Grayscale display for the current layer
L : Toggle Lightmap display
U : Toggle Unlit display
Alt : Use alternate behavior (depends on the active tool)

Projection Painting:

P : Projection tool
Shift + P : Toggle between Camera and Triplanar Projection
Shift + A : Reset Triplanar Projection
Ctrl + P : Bake Selected Texture Set

3D View:

1 : Default Shading
2 : Flat Shading
3 : Lighting/Shading
4 : Lighting/Shading with Textures
5 : Lighting/Shading with Material Colors
6 : MatCap (Material Capture) Shading

Selections:

Ctrl + Left-click : Add to Selection
Ctrl + Shift + Left-click : Subtract from Selection
Ctrl + I : Invert Selection