Pop-ups aren't inherently bad
Pop-ups (new web browser windows) that originate from web pages may have good purposes. They've just gotten a bad rap because they can also be used to display annoying advertising or expose computers to virus or spyware infection. The fact remains, however, that there are few things more inherently useful with modern computers than using multiple windows to best advantage. Particularly in FreeForm and EAPH program pages, new windows are used to help protect dynamic page content and prevent repeated page loadings.
If you experience pop-ups in an erratic manner and/or seemingly unrelated to the web sites you are visiting then you have a serious problem.
See: Keep your computer healthy
If you trust the web site, you can trust the pop-ups that originate from it
Anything seriously bad that could result from pop-ups will only occur when visiting either amateur web sites or sites that deliberately exist for the purpose of infecting the computers of those who visit it. Conversely, if you have determined a web site is genuine and reputable then pop-ups occuring there will not be dangerous. In other words, bad pop-ups will not originate from good web sites. See the side bar "keeping your computer healthy" if you experience pop-ups in an erratic manner or seemingly unrelated to the sites you visit.
By default disallow all pop-ups, allow them as needed at the sites you trust
The best way to defend yourself is to take a wait and see attitude. Block all pop-ups except at sites you have previously determined are safe and reputable. If, when using a reputable web site, you encounter performance problems such as links not working then set your pop-up blocker to allow pop-ups for that site.
Use only one (and only one) pop-up blocker that lets you know something has been blocked
Better yet, only use a pop-up blocker that not only tells you it has blocked something, but also provides the option to either allow pop-ups from that one page or permanently for the particular site. The best approach is to use (and only use) the pop-up blocker built into the web browser itself. Here are screen shots of the settings recommended for use with Microsoft Internet Explorer:
Accessing Microsoft Internet Explorer pop-up blocker settings
Notice the boxes that are checked. The "Show Information Bar" is important as it provides the option when a pop-up is blocked to go ahead and allow pop-ups from the page in which it was blocked, or to allow pop-ups from the entire web site. The filter level is set to it's highest setting so all pop-ups are blocked by default.
Be aware that add-on toolbars and Internet security software may also contain pop-up blockers
There is nothing more frustrating when using web sites than having things not work properly for you. Often as not that won't be a result of the programming at the web site, it will be a result of software or settings on your computer. Be very careful when installing add-on software that you retain control over what they do. In particular, look for and disable pop-up blocking and ad blocking in favor of the controls provided by the web browser itself.
Norton Internet Security software is probably the most notorious for not informing users what exactly it is doing. If you have that installed on your computer be especially aware that FreeForm and EAPH may not work properly for you unless you scrutinize and adjust its settings.