Note: ''Prior to Unity 5.3, this was the primary method of marking objects as dirty. From 5.3 onwards, with the introduction of Multi-Scene Editing, this function should no-longer be used for modifying objects in scenes. Instead, you should use Undo.RecordObject prior to making changes to the object. This will mark the object's Scene as dirty and provide an undo entry in the editor.''
Use EditorSceneManager.MarkSceneDirty when modifying files within the Scene with no added undo entries.
Also use SerializedObject.FindProperty, SerializedObject.Update, EditorGUILayout.PropertyField, and SerializedObject.ApplyModifiedProperties when using a custom editor to modify serialized properties on a component or an asset. When modified the component or asset will be marked as 'dirty' and have a created Undo state.
The only remaining use (which is used rarely) happens if a non-scene object is modified with other means and with no added undo entry. Use of this approach is unlikely.
The dirty flag is used internally to find changed assets that need to be saved to disk.