Use KeyRemap4MacBook:
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⌥⇥ is already used for inserting tabs in text fields, entering outline mode in TextEdit, and focusing elements in Safari.
Adding this to private.xml would change ⌘⇥ to ⌃⇥ and ⇧⌘⇥ to ⌃⇧⇥:
<autogen>__KeyToKey__ KeyCode::TAB, VK_COMMAND | ModifierFlag::NONE, KeyCode::TAB, ModifierFlag::CONTROL_L</autogen> <autogen>__KeyToKey__ KeyCode::TAB, VK_SHIFT | VK_COMMAND | ModifierFlag::NONE, KeyCode::TAB, ModifierFlag::CONTROL_L, ModifierFlag::SHIFT_L</autogen>
You can change the shortcuts of menu bar items from System Preferences: