What does "com.apple.*" mean in plist titles I have a programmable Logitech mouse, which allows me to assign different configurations to different applications, but ONLY .app files, but I wish to assign a profile to Java, which is a binary not enclosed in a .app file.

When I nosed around into its preference file, it only refers to some sort of identifier associated for that app. For example, instead of saying /Applications/Safari.app, it would only reference it as com.apple.safari.

What does com.apple.* mean? Is it some sort of application identifier? And, if so, how can I find the one for Java?
That particular naming structure is known as "reverse DNS" naming. (Like Apple's website is at apple.com, so their plist entries are com.apple.) This is done so that items are sorted by manufacturer before product if you sort by name. 

This nomenclature is used in Java packages (and other places) as well as OS X application identifiers.

If you want to specify Java as a whole, look for com.sun.* or com.oracle.*, as those are the two companies that have owned Java.