I received this response today from Thompson's when asking about Endnote's compatibility with ML:
I have read that X5 works but I'm not going to risk upgrading until I know for sure since I use Endnote every day. X6 comes out for Mac in September, so they might wait until then to announce something about ML.
Currently, none of the released versions of EndNote are tested for compatibility with Mac OS X Mountain Lion. Our development team is currently going through the process of testing EndNote with Mac OS 10.8. They will soon update the compatibility on our website here:
http://www.endnote.com/enosx.asp
However, at present we are unable to predict a date on when we are able to support this OS. The testing process is crucial before giving any concrete information on this. We apologize for any inconvenience this may cause.
I have read that X5 works but I'm not going to risk upgrading until I know for sure since I use Endnote every day. X6 comes out for Mac in September, so they might wait until then to announce something about ML.