First off, here's some short-hands used in the lists below:

LMB	- Click the left mouse button.
MMB	- Click the middle/wheel mouse button.
RMB	- Click the right mouse button.
Shift	- Hold down the Shift key while typing the listed key.
Space	- Hold down the Space key while typing the listed key.
Double	- Double tap the listed key.

Note: The hotkeys are case-sensitive. This means that if you accidentally turn Caps Lock on, then most functions will not work correctly. Because of this, a warning message will appear in the 3D window whenever you have Caps Lock on.

Common Keys

LMB            : rotate view
Arrow Keys     : rotate by 30 degrees
MMB            : pan
RMB            : zoom
LMB+MMB        : zoom
Wheel Roll     : zoom

Ctrl-Z         : undo

O              : toggle ortho/perspective projection

Pad5,Home      : focus view onto polys under mouse pointer
End            : focus view onto shell under mouse pointer

G              : mark paint polys
Double-G       : mark fill polys
Shift-G        : unmark paint
Double-Shift-G : unmark fill

H              : hide polys menu

G Menu

If you aim the mouse pointer at empty space, then type the G key, a menu of extra options appears towards the bottom of the graphics window.

LMB       : Click'n'drag the LMB to stretch a box over polys you want to mark.
RMB       : Click'n'drag the RMB to stretch a box over polys you want to unmark.
F         : Mark polys facing the camera.
H         : Hide all marked polys.
P         : Pin the vertexes of all marked polys.
Shift-P   : Unpin the vertexes of all marked polys.
S         : Unmark marked polys, and visa versa.
U         : Unmark all marked polys.
1-9       : Set brush size for G painting.
-/=       : Shrink and grow marked region.
Home      : Focus view on marked polys.
Enter     : Make the G menu go away.

H Menu

Whenever you type the H key, a menu of extra options appears towards the bottom of the graphics window.

LMB       : Click'n'drag the LMB to stretch a box over polys you want to hide.
RMB       : Click'n'drag the RMB to stretch a box; all polys outside are hidden.
G         : Hide all marked polys.
P         : Hide all unpicked shells.
S         : Hide all visible polys, and unhide all hidden polys.
U         : Make all polys visible.
Enter     : Make the H menu go away.

UV View

U/1            : toggle/set UV edit view

F              : hold down to flatten shell
Space-F        : start continuous flatten
Space          : stop continuous flatten
Shift-F        : bloat then reflatten

B              : flatten brush
O              : old flatten brush
-/=            : change brush size

C/W            : cut/weld seam
Shift-W        : toggle weld edges
Backspace      : unselect weld edges
M/Shift-M      : magnet snap weld edges

Enter          : attach/detach shells
Shift-D        : undrop shell back to Ed space
L              : toggle shell lock
  
T              : tag webbing edges
Shift-T        : toggle webbing edges
Backspace      : unselect webbing edges

P              : toggle pin
Double-P       : pin between two already pinned boundary points
Shift-P        : pin box menu

L/R Arrow      : flip shell in U
U/D Arrow      : flip shell in V

LMB            : click to pick/unpick single shell
               : click'n'drag to pick multiple shells
               : click in empty space to unpick all shells

Space-LMB      : rotate picked shells or marked polys
Space-MMB      : move picked shells or marked polys
Space-RMB      : scale picked shells or marked polys
Space-LMB+MMB  : as above
Tab            : hold down for finer control

Ctrl-MMB       : move single point
Ctrl-Shift-MMB : move connected points
Shift-MMB      : move points in circle

_/+            : change UV box size
L/R Arrow      : aim pointer at empty space to move UV box in U direction
U/D Arrow      : aim pointer at empty space to move UV box in V direction
Tab            : hold down for finer control

A              : toggle horizontal/vertical snap anchor
Shift-A        : turn off all anchors in shell 

Ctrl-L/R Arrow : aim pointer at edge to rotate shell so edge is horizontal
Ctrl-U/D Arrow : aim pointer at edge to rotate shell so edge is vertical

I              : tag straight edge - axis aligned 
Double-I       : tag extended
Shift-I        : as above
Backspace      : untag edge
Ctrl-I         : on tagged edge - remove all 'I' tagged edges from shell
                 on untagged edge - 'I' tag all similarly oriented edges
 
K              : tag straight edge - unaligned 
K              : toggle kink point
Double-K       : tag extended
Shift-K        : as above
Backspace      : untag edge
Ctrl-K         : on tagged edge - remove all 'K' tagged edges and points from shell
                 on untagged edge - 'K' tag all similarly oriented edges

When mouse pointer is aimed at shell boundary points:
 
  S            : toggle stack marker
  Double-S     : straighten between two stack markers
  Shift-S      : as above
 
When mouse pointer is aimed at shell interior polys:
 
  S            : copy UVs from light to dark mirror polys
  Shift-S      : swap light and dark mirror polys


When Brush Local Scale selected:
 
  4            : scale polys up
  5            : scale polys down
  4+5          : reset local scaling
 
When Brush Pin selected:
 
  4            : push UVs out and pin
  5            : pull UVs in and pin
  6            : smooth UVs and pin
  4+5          : unpin
 
Keys below are no longer supported:
 
  R            : relax brush
  Shift-R      : very relax brush
  X            : totally relax brush

Ed View

E/2            : toggle/set 3D edit view

C/W            : cut/weld seam
Shift-C/W      : cut/weld extended
Backspace      : unselect cut edges

Enter          : detach or split shell
D              : drop shell into UV space
Shift-D        : reattach shell

Shift-S        : split shell, or tag symmetry plane

3D View

3              : toggle/set 3D texture view

C/W            : cut/weld seam
Shift-W        : toggle weld edges
Backspace      : unselect weld edges

T              : cycle through textures
-/=            : scale texture

Shift-LMB      : click to pick/unpick single shell
               : click'n'drag to pick multiple shells
               : click in empty space to unpick all shells

S              : toggle smooth shading for SUBD surfaces