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. If you hold shift and press WASD while on the ladder your Kerbal will lean in that direction and when you press space you will jump in that direction.

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