Straight up, you have TWO choices.
1) Disable your PC's ability to view many java applets, or constantly changing your java settings on a per page basis.
2) Using third party software to either block pop-ups (But then you will also have problems with links that opn a new window) or running ADAWARE (or something similar)
I also run Win2KPro on a laptop and run ADAWARE at least twice a day. It cleans all the data miners and malware, thus reducing unwanted advertising. If it is AD pop ups that are a problem, ADAware removes the ads, without disabling your ability to view scripts and open links.
Cripple or control, it's up to you.
AdAware can be found here for free:
http://www.lavasoft.nu
A good antivirus engine is AVG Free edition:
http://www.grisoft.com
Clean it up and it will be faster and less annoying