The ShortcutMaker app lets you remap any keyboard shortcut sequence on a per-app basis…even with system keys. Want the windows key to be an extra CTRL modifier? Done. Need CTRL+C to paste instead of copy? No problem!

http://shortcutmaker.sourceforge.net/ (via http://www.addictivetips.com/windows-tips/redefine-global-app-specific-hotkeys-in-windows-shortcut-maker/)

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