Some people have asked for a list of all of the files you'd need to copy if you wanted to manually back up your full PinballY setup, including all of the media files and table information databases. Here's what you should save:
The Media and Databases folder locations depend on your option settings. You might want to read Files & Folders for full details, but here's the quick summary:
You don't need to back up the PinballY program files themselves, since you can always just do a fresh install to re-create those. But if you're not on a tight space budget for your backup media, the simplest thing is to just make a copy of your entire PinballY folder tree (plus your complete PinballX folder tree, if you're sharing media with PinballX).
For some recommendations about backing up your overall system, see Windows Setup in my pin cab build guide.