What are the differences in capabilities between the super-administrator and administrator?

The super_admin has access to all admininstrator APIs and also the multi-site functions.
If you go to the codex page, it will say so: http://codex.wordpress.org/Roles_and_Capabilities#Capability_vs._Role_Table

You can find the multisite functions here: http://codex.wordpress.org/Function_Reference#Multisite_functions

If you want to do a more fine-grain investigation of what it can call, I suggest you get familiar with the WP code. The funtion you should grep for is_super_admin

Hope this helps.

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