A partial list of the Kinesis Advantage / Controllermate / Emacs keybinding tweaks I've done.

kinesis.txt

Remapped on kinesis itself
--------------------------------------------------------------------------------
     caps lock             -> backspace (freq use)
     backspace             -> right gui/windows (freq use)
     left alt              -> return/enter (very infreq use)

     right ctrl            -> return/enter (freq use)
     right gui/windows     -> left gui
     enter                 -> right gui  (infreq use)
     
     left ctrl             == left gui/windows 
                              because I use the kinesis mac mode (=m)
         (freq use)
         (is then remapped immediately to f4)

Always remapped in controllermate (applied after kinesis hardware remaps)
--------------------------------------------------------------------------------
     left gui (aka left ctrl) -> f4
         (see above)
     right gui             -> activate Thumb Mode 1 (silences all other keys)
         (real keys = backspace & enter already remapped by kinesis)

     delete forward        -> activate Thumb Mode 2 (silences all other keys)
         (by left thumb)

     right-arrow           -> left ctrl
     left-arrow            -> left alt
     end                   -> left gui/windows

     page-down             -> right gui/windows
     down-arrow            -> right alt
     up-arrow              -> left ctrl


    # I also do some funky changes with these to make underscore more
    # handy, while keeping hyphen as top level key:
     \                     -> underscore
     shift hyphen          -> backslash \
     backtick              -> tilda
     left backslash        -> backtick
         (aka insert)

Thumb Mode 1 (very freq use)
--------------------------------------------------------------------------------
I also have a usb numeric keypad positioned under my right foot that
has most of its keys remapped to activate Thumb Mode 1.  So this could
also be called big-toe mode   Under my left foot I have the kinesis
foot pedal mapped to right-shift.  Using toe-mode allows me to use
these macros without tiring out my thumbs.


    v                      -> backspace
    =/+                    -> capslock
    ' (apostrophe)         -> return/enter

    # general navigation in emacs and bash, etc
    j                      -> left-arrow
    k                      -> down-arrow
    l                      -> right-arrow
    i                      -> up-arrow
   
    ;                      -> page-down
    p                      -> page-up
    m                      -> home
    ,                      -> end

    s                      -> ctrl left-arrow
    d                      -> ctrl down-arrow
    f                      -> ctrl right-arrow
    e                      -> ctrl up-arrow

    # macros for Awesome WM
    0                      -> gui+enter
    1                      -> gui+1
    2                      -> gui+2
    3                      -> gui+3
    4                      -> gui+4
    5                      -> gui+5
    6                      -> gui+6
    7                      -> gui+ctrl+return
    8                      -> gui+ctrl+k
    9                      -> gui+ctrl+j

    # I also used to have these two:
    #   .                      -> gui+k
    #   /                      -> gui+j    
    # but I'm currently experimenting with this intead:
    .                      -> (
    /                      -> )

    # macro for gnu screen
    u                      -> C-o (my screen command key rather than C-a)

    # macros for Emacs 
    right shift            -> C-l
    q                      -> [f5] (doubles as refresh in browser)
    x                      -> C-x C-s
    w                      -> [f4] (faster to reach)
    right ctrl             -> C-x C-s
    right gui              -> C-x v = (vc-diff, I usually just type this out)
    [                      -> C-x C-f
    ]                      -> M-x (remapped by emacs to smex)
    down-arrow             -> C-s
    up-arrow               -> C-r
    b                      -> C-x b
    g                      -> C-g
    t                      -> [f7]-0 (which toggles the mark)
    o                      -> C-x o
    space                  -> M-/
    a                      -> C-space
       (this is awesome in combination with my navigation keys above
        and quick access to C-y and M-w)
    backslash (right pinky)-> C-y
    hyphen (right pinky)   -> M-w

Thumb Mode 2 (less freq use)
--------------------------------------------------------------------------------
    # macro for nested copies of gnu screen
    u                      -> C-u (rather than C-a, or C-o)

    # macros for Emacs
    j                      -> [f2]-j (bound to windmove-left)
    k                      -> [f2]-k (bound to windmove-down)
    l                      -> [f2]-l (bound to windmove-right)
    i                      -> [f2]-i (bound to windmove-up)

    m                      -> [f2]-m (bound to flymake-goto-prev-error)
    ,                      -> [f2]-, (bound to flymake-goto-next-error)

    [                      -> C-u 5 C-x{ (shrink-window-horizontally)
    ]                      -> C-u 5 C-x} (enlarge-window-horizontally)

notes.txt

The emacs remappings are related to this:
http://bitbucket.org/tavisrudd/emacs.d/src/tip/dss-keybindings.el
(also see http://xahlee.org/emacs/keyboard_shortcuts.html)

Here's the OS X app I'm using:
http://www.orderedbytes.com/controllermate/
It's awesome, despite using a weird visual programming language for the rule definitions.  'AutoHotKey' seems to be the Windows equivalent, though I don't think it allows you to define separate rulesets per usb device.

I haven't found anything exactly like it for Linux, but these might work:
- http://usbhotkey.sourceforge.net/
- http://code.google.com/p/autokey/
 (seems hard to install without a debian based system)
- http://www.autohotkey.com/forum/topic54494.html
- or AwesomeWM's own keybinding system

To get something equivalent to my controllermate setup you would need:

- the ability to remap a single key into a multiple-key output sequence
(I know the Kinesis can do this at the hardware level, but I don't trust its potentially volatile memory and hate the opaque interface for defining them)

- the ability to activate sub-maps like I'm doing with my thumb-modes.

- the ability define separate maps per usb input device.  Hopefully usbhotkey can do that.

Here's some other related notes:
http://debian-user.blogspot.com/2009/01/autohotkey-for-linux.html
http://www.hotsolder.com/2008/08/autohotkey-for-linux-sort-of.html