We have finished our testing of ChemDoodle on Mac OS X 10.8, Mountain Lion, and everything works as expected. ChemDoodle will continue to work for you on your mac, even after you update to Mac OS X Mountain Lion. We also properly sign our application to comply with Gatekeeper, so there is no need to worry about security issues when using ChemDoodle. As a note, you should leave the Gatekeeper settings at their default secure values. Do not follow any instructions to reduce the security settings on your Mac, even if other vendors say to do this to get their software to work (such as with Java applets). Those vendors should properly adhere to Gatekeeper. If you are looking for an alternative to poor performing Java applets, please check out the ChemDoodle Web Components.
Also, keep in mind that we will be dropping support for Mac OS X 10.5, Leopard, with the release of ChemDoodle 5. ChemDoodle 5 will require Java 1.6+, which is fully supported on Mac OS X 10.6+ (Snow Leopard, Lion, Mountain Lion). So now is a good time to upgrade your operating system.
We regard Mac OS X as a primary platform and will always support it. With ChemDoodle, you can be confident that your work will be unimpeded by major OS updates.