I've only noticed a few little anomalies with IE 9 so far.
With the skin on this site it was showing the fonts in the menu really bold and it was throwing off the menu rendering compared to other browsers so I had to add an override file for IE 9 (implemented like we have for other versions of IE), and make the font used there a little less bold. I fixed this first thing yesterday after I installed IE 9 and noticed it. The JQueryUI skin also needed some reduction in boldness for headings.
The most annoying thing I've discovered so far is a problem with the menu on this site, if you right click a menu link you don't get the option to open the link in a new tab (in fact you get no option to open the link at all with right clicking). I've noticed the same thing in gmail, where when using Chrome I can right click the google calendar link at the top of gmail and open it in a new tab, but in IE 9 I can't.
In the skin for this site I've narrowed down the problem is caused by the use of display:block; on the span element inside the link. The span is used for hanging a background image for the right corner of the tab. If I change it to display:inline the right clicking works on the link but the style is not right, whereas with display:block the style is right but it seems that right clicking is interpreted as clicking the span and not the link, even though the span is inside the link. Haven't figured out a good solution for this one yet.
I haven't seen this problem in other skins so far but have not checked them all exhaustively.
Best,
Joe