In general, popup refers to any UI element that floats above a window or application surface. This may include tooltips, context menus, and modal dialog windows.
It might exist within the current window/page, or it may be a completely new window.
The popup may be an alert, a confirmation interface, an advertisement, and more.
Some types of popups have become such a nuisance, that popup blockers have been a favorable tool for web users.