Should this be tagged "Applications"?

I use a shell script like this to configure the keyboard shortcuts:

defaults write -g NSUserKeyEquivalents '{
"Minimize"="\u200b";
"Minimize All"="\u200b";
}'

defaults write com.apple.finder NSUserKeyEquivalents '{
"Show Package Contents"="@\r";
"Tags..."="@t";
}'

defaults write -app Safari NSUserKeyEquivalents '{
"Show Previous Tab"="@j";
"Show Next Tab"="@k";
"Mail Contents of This Page"="\u200b";
}'

defaults write -app Mail NSUserKeyEquivalents '{
"\033Format\033Indentation\033Decrease"="^\Uf702";
"\033Format\033Indentation\033Increase"="^\Uf703";
}'

The shortcut strings use the same format as in DefaultKeyBinding.dict. For example \Uf702 is the left arrow key.

-app doesn't work with some applications like Finder or Notes.

You can disable a shortcut by assigning the menu item to for example \u200b (ZERO WIDTH SPACE). nil would be triggered by n in some applications like Audacity, \0 would be triggered by any key in Safari in 10.9, and \1 would be triggered by the home key.

If you specify a menu item as Format->Indentation->Increase in System Preferences, it is stored as \033Format\033Indentation\033Increase.