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My GNOME keyboard settings do two main things:

  • Switch CMD and CTRL (I'm on a Macbook)
  • Give me a third level (for special characters)

This is really the only functionality I'm missing in Fluxbox. Any way to activate it without running GNOME?

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If, by "third level", you mean using eg. the American Internation keyboard layout, you can set up your system to use it by default.
On Debian (and quit possibly siblings; (X|K)Ubuntu, Mint and so on), you can put the following in /etc/default/keyboard:

XKBMODEL="pc105" #physical keyboard model
XKBLAYOUT="us" # keyboard layout
XKBVARIANT="altgr-intl" # keyboard layout variant
XKBOPTIONS="terminate:ctrl_alt_bksp,numpad:microsoft" # terminate X on
    # CTRL+ALT+DEL, and use Microsoft style numpad

There's probably a lot of other places for keyboard configuration on other flavours of Linux – on Gentoo/Funtoo it's in /etc/conf.d/keymaps

Regarding switching the CMD and CTRL keys, I think it's already been answered here: Map "windows" key on keyboard to "ctrl".
Keeping in line with the above configuration, just add altwin:ctrl_win to the XKBOPTIONS line, like this:

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