The update window allows you to keep MeGUI and its components up to date. Whenever you run MeGUI, it will automatically check for updates and prompt you if there are any available. You can also run the updater from the Tools menu.
When the updater window opens, it will automatically poll the webserver for any updates. If updates are available, it will automatically select them in the list, ready for you to click Update.
If you do not wish to update a certain component, you can right click on the item and choose "Ignore updates for this file". Any future updates will not be automatically suggested. You can undo this by right clicking and selecting "Ignore updates for this file" again.
The download cache for MeGUI is located at megui.org/auto or here as mirror. An xml file (update.xml) is downloaded which contains a list of components and their latest versions. If the latest version is newer than the version MeGUI has recorded as downloading, it will prompt for updating. Keep in mind MeGUI determines what requires updating by its internal records, not by reading file version from the files or anything.