You can have a Hyper key (in X11, at least!)

http://computing.fnal.gov/docs/products/xemacs/v21_1/xemacs....

Depending on your keyboard layout, the "Menu" key makes a good Hyper, and if you've set up Caps Lock as an extra Ctrl key, you can remap your left Ctrl key to something useful.

You can also separate Alt and Meta to different keys.

A quick emacs session will show you whether your new modifier keys are working as intended.

IIRC you can do similar for the (text-mode) Linux console as well.