OS 3.1 rules :-)
It only lacks the Reaction GUI and OS 3.5 icons: i really dislike softwares that make use of these, forgetting about OS 3.1.
Hmm..OS 3.9 has large hard drive support, TCP stack, email, web browser, Action, updated multiview, updated dataypes, 24 bit printer support, cd file system and atapi support, built in dock, new icon information with drag an drop icon update, animated scrolling of icons within windows, correct aspect ratio of window's horizontal scroll bar. Probably a fair few other things that aren't visible on the surface.
You could do most of this stuff with 3rd party utilities, but its nice to have it all there for you when you boot.
Having said that I I use a 4 color 3.1 workbench and 3.1 ROM, flies. Eye candy no longer matters to me.
If you're using a 3.0 ROM with 3.1 I think its its worth getting the 3.1 ROM, seems more stable and screen re-draws seem faster.