Links don't work

Probably this won't help, but I went through something with Earthlink and its popup blocker. Some links would open, but not within this particular site. It was a bit overagressive, and maybe the one you're using is as well.

lotsa luck

Are there other problems that started at the same time as these? Reporting those too could help with tracking down a cause. Also, is there anything you did recently that could've led up to these problems?

Java is unrelated to the popups not showing up. (Actually, depending on what type of "popups" you're talking about Java could be related but I suspect it's not the case here.) Javascript being turned off, on the other hand, could be what's causing many of your popups to not show up, but more likely an overzealous popup blocker has been installed on your computer recently. If so, find it and disable it or uninstall it. Many popup blockers allow popups when you click a link while holding down the Ctrl key...you should try that out first.

As for Edit->Find not working, possibly IE is damaged & needs to be reinstalled. It's a strange problem.