I have looked everywhere but I can't find an answer. What is the pcsx2 binary file? It says it's compressed, which tells me its a smaller file, but it's only 2 mb smaller! That's not much of a difference. Besides that, I've tried both the binary, regular version, and beta of the new one. The normal and beta have some different menus (such as the cdddvd config). But what's the real difference between the normal/beta and binary?

There are 2 things to download:
0.9.6 release,the installer or the binary
Beta release,the installer or the binary

Binaries are the actual files with no installer,which you simply unzip and run pcsx2.exe,while the installer provides you some installation options and an uninstaller.