Cut-scenes are special pre-scripted portions of the game, in which players have no control (except possibly being given a dialog with choices in it). These are fully module-dependent, as they are basically the module's author temporarily taking over the game. BioWare uses them only occasionally, often when the plot calls for showing an event in which the player's character is not directly involved. Cut-scenes can be aborted by pressing the <Esc> key unless the module's author has blocked this.
During a cut-scene, the game's graphical user interface is hidden, leaving just the view of the game's world. Furthermore, moving the mouse over something will not highlight that object, unlike what happens if one hides the graphical interface during normal gameplay (using the 'h' key by default).