There are a few Drupal-specific stuff that would be great to see in the wysiwyg toolbar but that won't be found in any out-of-the-box Rich Text Editor.
1) Internal links
Drupal has nodes. A user in MediaWiki, for instance, uses [ [Name of the article] ] to create an internal link to another article. We could adopt a similar concept and create a "link internal" that open an auto-complete form, allowing the user to select a node in the list. In fact, it isn't a new idea and it's been already implemented in a contributed project: http://drupal.org/project/easylink
It's very simple stuff, but also a tremendous usability enhancement if in core. I plan to work on it once the WYSIWYG for D7 takes shape.
2) Input type selector in toolbar
Instead of displaying input formats below the textarea, why not display it as a button/select in the editor toolbar? It makes perfect sense, since the buttons in the toolbar change accondingly to the input format.
3) AJAX'ed preview
Instead of a button "preview" in the bottom of page, why not a preview tab above the textarea, alongside the tabs "edit" and "code"?
Got the ideas or d'you need mockups?