There's been some progress with the monobook skin recently, new things are basic rtl support and user styles.
You can tweak styles in the monobook skin by adding a page called 'monobook.css' as a subpage of your user page. My test css is at http://test.wikipedia.org/wiki/User:Gwicke/monobook.css for example.
Similar with js, the it's called monobook.js in that case. Other skins don't have the links in the header currently, but those are easy to add.
The css and js pages are editable only to the user and developers, they appear protected to anybody else.
The wiki src is retrived with a new method to get the raw wiki text: http://test.wikipedia.org/wiki/User:Gwicke/monobook.css?action=raw&ctype...
Allowed ctypes are text/css, text/javascript, text/x-wiki and application/x-zope-edit. Any of these return the plain wiki src, just the content header differs. A charset option is optional, e.g. &charset=utf-8.
Brion and me have added an RTL stylesheet to monobook, it seems to work fine in Opera 7.23, Mozilla/Firefox, IE5.5 and mostly IE6. Screenshots at http://wikidev.net/MonoBook_RTL.