Your idea of using xbindkeys sounds good:

in your .xbindkeysrc add a new keybinding:

"app_specific_keys.sh"

   Control+s

This will execute "app_specific_keys.sh" when you press ctrl+s.

Now you need to define the script. It should get the active window and from that the name of the app which currently has the focus:

xprop -id `xdotool getactivewindow` |awk '/WM_CLASS/{print $4}'

This would do the trick: it asks xdotool for the active window, then asks xprop for all properties of the window with the given id, and then reduces the very verbose output to the name of the application (actually its class). If you run this in a gnome-terminal you would get

"Gnome-terminal"

Now you need to define actions for your applications:

if [ $N = '"Gnome-terminal"' ]; then                                                    

    xdotool key --clearmodifiers ctrl+s                                                          

else                                                                            

    xdotool key --clearmodifiers ctrl+d                                                          

fi  

So together, the script "app_specific_keys.sh" could look like this:

#!/bin/bash                                                                     

W=`xdotool getactivewindow`                                                     

S1=`xprop -id ${W} |awk '/WM_CLASS/{print $4}'`                                 

S2='"Gnome-terminal"'                                                           

if [ $S1 = $S2 ]; then                                                          

   xdotool key --clearmodifiers ctrl+d                                             

else                                                                            

   xdotool key --clearmodifiers ctrl+s                                          

fi  

This should work, but as in this question, I have to admit that it does not. Probably because one of Compiz, Unity, Global Menu does not work well with the --clearmodifiers option of xdotool. A workaround would be to add a sleep in front of your script in oder to be able to release the keys yourself:
In your .xbindkeysrc change to this keybinding:

"sleep 0.5; app_specific_keys.sh"

   Control+s

As a sidenote: this will not work, if you want to change keys for programs which run in a terminal (e.g. vi or emacs in console mode). The returned application class would still be "Gnome-terminal".

Hope that helps.