Edit cms/javascript/tinymce.template.js – you can use any configuration options you find at http://wiki.moxiecode.com/index.php/TinyMCE:Configuration
I was trying to use this to enable force_br_newlines but with no luck – although the other settings seem to work okay.
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In version 2.4, it looks like this has moved to /cms/_config.php – which makes a lot more sense to me.