Make the CTRL and Super/CMD keys behave like on OS X

Here's how I've done it on my MAC book running Kubuntu :

1. Use xmodmap to swap command key and ctrl key globally.
   a) Put the following in a file ~/.Xmodmap

   clear control  
   clear mod4  
   
   keycode 105 =  
   keycode 206 =  
   
   keycode 133 = Control_L NoSymbol Control_L  
   keycode 134 = Control_R NoSymbol Control_R  
   keycode 37 = Super_L NoSymbol Super_L  
   
   add control = Control_L  
   add control = Control_R  
   add mod4 = Super_L  
   

   b) Run the following command :

   $ xmodmap ~/.Xmodmap 
   

   This will make all your application use Command + .. instead of ctrl + .. except terminal
   Remember, your command key is now ctrl key

2. Modify shortcut keys for Terminal

a) In terminal application, go to "Configure Shortcuts"
b) Change the shortcuts for the following :

• Cut - To 'Command + c '

• Paste - To 'Command + v '

• Interrupt - To 'Ctrl + c '

• New Tab - To ' Command + t'

• Close Tab - To 'Command + w'

• Any other key your are particular about ..

3. Disable Meta key from invoking the app launcher [ kubuntu only ]

Add the following to ~/.config/kwinrc

[ModifierOnlyShortcuts]  
Meta=

You actually CAN use the Cut/Copy/Paste-Hotkeys in a terminal: You just have to additionally use the Shift key:

Copy: Ctrl+Shift+C

Paste: Ctrl+Shift+V

Cut: Ctrl+Shift+X

Some command editing shortcuts:

Delete one word: Alt+Backspace

Move cusrsor one word left/right: Ctrl+←/Ctrl+→

If you want to use the Super key as a modifier, there is no possibility to do so in GTK-based desktop environments. If this is a important feature for you, you could give KDE a try.