I'm wondering if there is a way to change the wallpaper from a java
program, and/or refresh the wallpaper somehow, or maybe overwrite the
wallpaper .gif or .jpg through the filesystem in order to modify the
wallpaper?
Keep in mind that there is not going to be any native Java functions for
setting wallpaper since this is system specific.
All of the following is assuming you are referring to a Win32 OS:
If this is a personal project, you could just make it replace your wallpaper
file - but this would not instantly update your screen (it would need to
reboot - and sometimes Windows cache's the image somehow, making file
replacement unpredictable even across boots!)
Google searches quickly turned up Visual Basic and C++ examples.
If I were you I would create a small DLL file with a function for setting
the wallpaper from the examples of the C++ code found on the web, and then
use JNI to integrate it with Java.