Pop-ups are additional browser windows that are opened (usually) via JavaScript. A function frequently responsible for opening the popup window is window.open
.
Most browsers have popup-blocking features because popups are annoying. As mentioned in the comments, shady websites frequently throw up numerous windows with ads or malware. Most popup blockers only allow popups if the window was created in an event handler that runs in response to a user action. For example, a popup blocker might allow a new window to appear when you click on a button, but not in response to a timer.
Super User, to my knowledge, never creates popups. Therefore, it's very likely that there is other software on your computer that is injecting content into otherwise "healthy" web pages. Please see How can I remove malicious spyware, malware, adware, viruses, trojans or rootkits from my PC? Once you clean out the malicious software, you will probably barely ever see a "popup blocked" message.