Natural Docs 0.95 now has a second, framed output format.  Use -o FramedHTML instead of -o HTML to use it, but make sure you use the -ro option the first time.  While some people don't like frames, this has the benefit of not requiring every output file to be updated whenever the menu changes.  Take a look.

Did I mention there was an -ro option?  It only rebuilds the output files, which is faster than -r which rebuilds everything.

0.95's HTML has better compatibility with older IE releases thanks to its new ability to specify browser-specific styles in a single CSS file.  This allows you to change styles just for a specific browser or browser version and thus work around quirks better.  You should definitely upgrade if just for this reason.

Mozilla users are also getting rounded corners, as you can see on the front page if you're using it.  It's a non-standard extension though, and will be replaced by the CSS 3 equivalent when it's finalized and supported.

The threshold for when menu groups start defaulting to collapsed has been lowered a bit, which should be better for the most common monitor resolutions.

There's been some changes to the CSS structure of the HTML, so 0.95 will automatically rebuild all output files generated with previous releases and update the CSS files when it's first run.  You only have to care about this if you're using your own custom CSS files, in which case you should read the Page Structure and Browser Styles sections of the updated CSS guide.

Next release is 1.0.  :)