Bevel: 
None: Height 
Ctrl: Inset 
Ctrl Shift: Inset, slower increase, snaps to 0 if value is < 0.2 
Shift: Extrude slower increase, snaps to 0 if value is < 0.2 
Alt: Modes 
First Left Click: Start Tool 
Left Click: Accept 
Right Click: Cancel

Chamfer: 
None: Amount 
Ctrl: Segments 
Shift: Amount, slower increase 
Alt: Tension 
First Left Click: Start Tool 
Left Click: Accept 
Right Click: Cancel

Interactive Symmetry Modifier: 
If you have an edge or vert selection it will try to guess the direction and plane of the symmetry based on the distance of the selection

Interactive Symmetry Modifier: 
If you select a face it will align the symmetry axis to the face normal.

Interactive Set Cylindrical Sides: 
Select a loop, run it and make a click to active the tool. It will try to guess the axis of the lathe for you. 
Requires the pivot to be in the center of cylinder. 
None: Segments 
Shift: Segments + 2

Smart Pivot: 
Make a selection and run it, it will center the pivot to your selection.

Interactive Quad Chamfer Modifier: 
This requires the Quad Chamfer Modifier by Marius in order to work. 
None: Amount 
Ctrl: Segments 
Shift: Amount, slower increase 
Alt: Tension 
First Left Click: Start Tool 
Left Click: Accept 
Right Click: Cancel

Interactive Shell Modifier: 
None: Change Symmetry Axis 
Shift: Slower Increment 
Ctrl: Segments 
Alt: Mode (Single/Double Sided) 
Left Click: Accept 
Right Click: Cancel 
You can edit the results if you run the script again as it controls the modifier

Smart Rotate (Positive and Negative): 
Works based on the direction of the normal under your cursor, rotating the object 45 degrees in the plane the object normal is pointing at. Only works for the X,Y and Z Plane.

Smart Align: 
Works based on whats under your cursor when you run it. If you are close to an Axis It will center it to that axis. If there's an object under your cursor you can click it and the Align Dialog will pop up

Plane: 
None: Divisions 
Alt: - 
Ctrl: Size 
Shift: Size (lower increment) 
Alt+ Ctrl + Click: Align to axis 
First Left Click: Place object 
Left Click: Accept 
Right Click: Cancel

Box: 
None: Divisions 
Alt: - 
Ctrl: Size 
Shift: Size (lower increment) 
Alt+ Ctrl + Click: Align to axis 
First Left Click: Place object 
Left Click: Accept 
Right Click: Cancel

Cylinder Creation: 
Nothing Pressed: Segments +1 
Alt: Height 
Ctrl: Radius 
Shift: Segments +2 
Alt+ Ctrl + Click: Align to axis 
First Left Click: Place Obj 
Left Click: Accept 
Right Click: Cancel

QuadSphere: 
None: Segments 
Ctrl: Size 
Shift: Slower Size 
Alt+ Ctrl + Click: Align to axis 
First Left Click: Place Obj 
Left Click: Accept 
Right Click: Cancel