Key Bindings

Cesrate

In Flight
Double Tap Brake : Parking Brake
Alt+Time warp Keys : Force "Physics" warp
Alt+L : Toggle Staging Lock (Disable spacebar / Stage key)
Alt+Pitch/Yaw/Roll : Trim (Move the "zero position")
Alt+X : Reset Trim

In EVA
Hold left mouse button to freely orient your Kerbals in ANY direction.
Hold Shift (or presumably, the key you bind running to) while letting go of a ladder to jump backward instead.

VAB/SPH
WASDQE : Rotate part. Usually in the wrong direction or along the wrong axis. Think of shaving in a mirror or a USB port
Shift+WASDQE : Fine rotation (5° increments)
Space : Reset rotation
Shift+Click on any part of the ship : Select the whole ship (Like if you clicked on the pod)
Alt+Click on a part: Clone Sub-tree (clone a part and all it's "children")
Ctrl+Click on a part : Navigate to that part in the parts list
X : Cycle through symmetry modes
C : Toggle Snap to Angles
Ctrl+Z : Undo
Ctrl+Y : Redo

Anywhere
Ctrl+Alt+Shift+D : Toggle Debug "Cheats" Window
Alt+F2 : Toggle Debug Console Window