Every desktop environment that I'm familiar with (OSX, KDE, Gnome) has a built-in password manager to hook into, that stores the data encrypted and prompts the user for a master password in some configurable way. I'm guessing that if the OSX and Linux variations of Chrome get any traction, hooking into the password manager will probably be done.
I have no idea if Windows has a password manager, but I don't know why it wouldn't.
Even if it encrypts the password before storing them on disk, the encryption/decryption key are necessarily on disk anyways, no?