Is there a way to set an Application Shortcut in the Keyboard Preference Pane via Terminal?
You could use the defaults command on ~/Library/Preferences/com.apple.symbolichotkeys.plist.

The file's structor seems a bit overly complex, but:*


  131072: Shift
   262144: Control
   524288: Option
   1048576: Command  
  
  Add modifier values together in the 3rd parameter to combine them.  
  
  { AppleSymbolicHotKeys = {  
  
  # Move focus to the menu bar - Control, F2
   7 = { enabled = 1; value = { parameters = ( 65535, 120, 262144 ); type = standard; }; };   
  
  # Move focus to the Dock - Control, F3
   8 = { enabled = 1; value = { parameters = ( 65535, 99, 262144 ); type = standard; }; };   
  
  # Move focus to active or next window - Control, F4
   9 = { enabled = 1; value = { parameters = ( 65535, 118, 262144 ); type = standard; }; };   
  
  # Move focus to window toolbar - Control, F5
   10 = { enabled = 1; value = { parameters = ( 65535, 96, 262144 ); type = standard; }; };   
  
  # Move focus to floating window - Control, F6
   11 = { enabled = 1; value = { parameters = ( 65535, 97, 262144 ); type = standard; }; };   
  
  # ??? - Control, F1
   12 = { enabled = 1; value = { parameters = ( 65535, 122, 262144 ); type = standard; }; };   
  
  # Change the way Tab moves focus - Control, F7
   13 = { enabled = 1; value = { parameters = ( 65535, 98, 262144 ); type = standard; }; };   
  
  # Turn zoom on or off - Command, Option, 8
   15 = { enabled = 1; value = { parameters = ( 56, 28, 1572864 ); type = standard; }; };   
  
  # Zoom in - Command, Option, =
   17 = { enabled = 0; value = { parameters = ( 61, 24, 1572864 ); type = standard; }; };   
  
  # Zoom out - Command, Option, -
   19 = { enabled = 0; value = { parameters = ( 45, 27, 1572864 ); type = standard; }; };   
  
  # Reverse Black and White - Command, Control, Option, 8
   21 = { enabled = 1; value = { parameters = ( 56, 28, 1835008 ); type = standard; }; };   
  
  # Turn image smoothing on or off - Command, Option, \
   23 = { enabled = 0; value = { parameters = ( 92, 42, 1572864 ); type = standard; }; };   
  
  # Increase Contrast - Command, Control, Option, .
   25 = { enabled = 1; value = { parameters = ( 46, 47, 1835008 ); type = standard; }; };   
  
  # Decrease Contrast - Command, Control, Option, ','
   26 = { enabled = 1; value = { parameters = ( 44, 43, 1835008 ); type = standard; }; };   
  
  # Move focus to the next window in application - Command, backtic
   27 = { enabled = 1; value = { parameters = ( 96, 50, 1048576 ); type = standard; }; };   
  
  # Save picture of screen as file - Command, Shift, 3
   28 = { enabled = 1; value = { parameters = ( 51, 20, 1179648 ); type = standard; }; };   
  
  # Copy picture of screen to clipboard - Command, Control, Shift, 3
   29 = { enabled = 1; value = { parameters = ( 51, 20, 1441792 ); type = standard; }; };   
  
  # Save picture of selected area as file - Command, Shift, 4
   30 = { enabled = 1; value = { parameters = ( 52, 21, 1179648 ); type = standard; }; };   
  
  # Copy picture of selected area to clipboard - Command, Control, Shift, 4
   31 = { enabled = 1; value = { parameters = ( 52, 21, 1441792 ); type = standard; }; };   
  
  # All Windows - F9
   32 = { enabled = 1; value = { parameters = ( 65535, 101, 0 ); type = standard; }; };   
  
  # Application Windows - F10
   33 = { enabled = 1; value = { parameters = ( 65535, 109, 0 ); type = standard; }; };   
  
  # All Windows (Slow) - F9
   34 = { enabled = 1; value = { parameters = ( 65535, 101, 131072 ); type = standard; }; };   
  
  # Application Windows (Slow) - F10
   35 = { enabled = 1; value = { parameters = ( 65535, 109, 131072 ); type = standard; }; };   
  
  # Desktop - F11
   36 = { enabled = 1; value = { parameters = ( 65535, 103, 0 ); type = standard; }; };   
  
  # Desktop (Slow) - F11
   37 = { enabled = 1; value = { parameters = ( 65535, 103, 131072 ); type = standard; }; };   
  
  # ??? - Command, Option, T
   50 = { enabled = 1; value = { parameters = ( 116, 17, 1572864 ); type = standard; }; };   
  
  # Move focus to the window drawer - Command, Option, quote
   51 = { enabled = 1; value = { parameters = ( 39, 50, 1572864 ); type = standard; }; };   
  
  # Turn Dock Hiding On/Off - Command, Option, D
   52 = { enabled = 1; value = { parameters = ( 100, 2, 1572864 ); type = standard; }; };   
  
  # ??? - F14
   53 = { enabled = 1; value = { parameters = ( 65535, 107, 0 ); type = standard; }; };   
  
  # ??? - F15
   54 = { enabled = 1; value = { parameters = ( 65535, 113, 0 ); type = standard; }; };   
  
  # ??? - Option, F14
   55 = { enabled = 1; value = { parameters = ( 65535, 107, 524288 ); type = standard; }; };   
  
  # ??? - Option, F15
   56 = { enabled = 1; value = { parameters = ( 65535, 113, 524288 ); type = standard; }; };   
  
  # Move focus to the status menus - Control, F8
   57 = { enabled = 1; value = { parameters = ( 65535, 100, 262144 ); type = standard; }; };   
  
  # Turn VoiceOver on / off - Command, F5
   59 = { enabled = 1; value = { parameters = ( 65535, 96, 1048576 ); type = standard; }; };   
  
  # Select the previous input source - Command, Option, Space
   60 = { enabled = 1; value = { parameters = ( 32, 49, 1572864 ); type = standard; }; };   
  
  # Select the next source in the Input Menu - Command, Option, Shift, Space
   61 = { enabled = 1; value = { parameters = ( 32, 49, 1703936 ); type = standard; }; };   
  
  # Dashboard - F12
   62 = { enabled = 1; value = { parameters = ( 65535, 111, 0 ); type = standard; }; };   
  
  # Dashboard (Slow) - F12
   63 = { enabled = 1; value = { parameters = ( 65535, 111, 131072 ); type = standard; }; };   
  
  # Show Spotlight search field - Command, Shift, Space
   64 = { enabled = 1; value = { parameters = ( 65535, 49, 1179648 ); type = standard; }; };   
  
  # Show Spotlight window - Control, Shift, Space
   65 = { enabled = 1; value = { parameters = ( 65535, 49, 393216 ); type = standard; }; };   
  
  # Dictionary MouseOver - Command, Shift, E
   70 = { enabled = 1; value = { parameters = ( 101, 2, 1179648 ); type = standard; }; };   
  
  # Hide and show Front Row - Command, Esc
   73 = { enabled = 1; value = { parameters = ( 65535, 53, 1048576 ); type = standard; }; };   
  
  # Activate Spaces - F8
   75 = { enabled = 1; value = { parameters = ( 65535, 100, 0 ); type = standard; }; };   
  
  # Activate Spaces (Slow) - Shift, F8
   76 = { enabled = 1; value = { parameters = ( 65535, 100, 131072 ); type = standard; }; };   
  
  # Spaces Left - Control, Left
   79 = { enabled = 1; value = { parameters = ( 65535, 123, 262144 ); type = standard; }; };   
  
  # Spaces Right - Control, Right
   81 = { enabled = 1; value = { parameters = ( 65535, 124, 262144 ); type = standard; }; };   
  
  # Spaces Down - Control, Down
   83 = { enabled = 1; value = { parameters = ( 65535, 125, 262144 ); type = standard; }; };   
  
  # Spaces Up - Control, Up
   85 = { enabled = 1; value = { parameters = ( 65535, 126, 262144 ); type = standard; }; };   
  
  # Show Help Menu - Command, Shift, /
   91 = { enabled = 0; };
   92 = { enabled = 0; };
   98 = { enabled = 0; value = { parameters = ( 47, 44, 1179648 ); type = standard; }; };   
  
  # Switch to Space 1 - Control, 1
   118 = { enabled = 1; value = { parameters = ( 65535, 18, 262144 ); type = standard; }; };   
  
  # Switch to Space 2 - Control, 2
   119 = { enabled = 1; value = { parameters = ( 65535, 19, 262144 ); type = standard; }; };   
  
  # Switch to Space 3 - Control, 3
   120 = { enabled = 1; value = { parameters = ( 65535, 20, 262144 ); type = standard; }; };   
  
  # Switch to Space 4 - Control, 4
   121 = { enabled = 1; value = { parameters = ( 65535, 21, 262144 ); type = standard; }; };   
  
  122 = { enabled = 0; };
   123 = { enabled = 0; };
   124 = { enabled = 0; };
   125 = { enabled = 0; };
   126 = { enabled = 0; };
   127 = { enabled = 0; };
   128 = { enabled = 0; };
   129 = { enabled = 0; };
   130 = { enabled = 0; };
   131 = { enabled = 0; };
   132 = { enabled = 0; };
   133 = { enabled = 0; };
   134 = { enabled = 0; };
   135 = { enabled = 0; };
   136 = { enabled = 0; };
   137 = { enabled = 0; };
   138 = { enabled = 0; };
   139 = { enabled = 0; };
   140 = { enabled = 0; };
   141 = { enabled = 0; };
   142 = { enabled = 0; };
   143 = { enabled = 0; };
   144 = { enabled = 0; };
   145 = { enabled = 0; };
   146 = { enabled = 0; };
   147 = { enabled = 0; };
   148 = { enabled = 0; };
   149 = { enabled = 0; };
   }; }  


Two decent sources:


http://hintsforums.macworld.com/showthread.php?t=114785
http://krypted.com/mac-os-x/defaults-symbolichotkeys/


*this is a bit dated