Which browser is this, and what version of Java?
The Mozilla corporation disabled my Firefox browser's Java Deployment Toolkit plugin, (remotely), a few days ago because it has been deemed as 'vulnerable' to malware attack. I then decided, perhaps later than I should have done, to uninstall all Java from my system then install the latest version, 126.96.36.199 . It might be time for you to do the same.
Also, you say you just wait. What happens if you click the "Click to end" option?
Whenever I go to a site and click on a link that opens a new window the new window pops up and say "loading" then it will stop and I get this error message "Java Platform SE6 U19 & U20 unresponsive, click to end". I don't do anything but wait. After about 30 sec. the window opens up and everything works fine, very annoying. I have a HP Pavilion Notebook, running Vista.