To get the dialog up: Keyboard Settings --> Layout Settings --> Options
Caps Lock key behavior --> Caps Lock is disabled
I can't decide if I like this or not: "Make Caps Lock an additional Super" seems to make Gnome Shell use Caps Lock instead of the window key and the window key can be used as a modifier as normal (i.e. no need to do Super+Space,Super+Space to bring up gnome-do).
Not really sure why this isn't on by default. It's not like anyone's going to hit it by accident:
Key sequence to kill the X server --> Control + Alt + Backspace
Numpad only (does anyone use those keys as anything else?):
Miscellaneous compatibility options --> Numeric keypad keys always enter digits (as in Mac OS) (this seems like NumLock always being on which won't screw things up if the keyboard doesn't have a dedicated numpad)
Outside of Gnome: edit /etc/default/keyboard (in Debian, at least) and refer to /usr/share/X11/xkb/rules/xorg.lst for settings
EDIT: in 3.8, this stuff is in the Tweak Tool under "Typing".