I have Empathy installed on my Ubuntu 12.04 with Gnome 3. I appear to be online in the chat networks when my computer is connected to the internet. However, I did not even start Empathy, at least not manually.
How can I change this behaviour?
This is the default behavior of gnome shell and allows (at least in theory) for better integration with the new GUI. You can log out of chat by using the selection box under your name in the top-right menu (change setting to unavailable).
Under 'preferences' in Empathy is a box marked 'Automatically connect at startup'. If you uncheck this, Empathy should not sign you in to your chat accounts at log in.
If you just only want to make Empathy start but not login in your account, check their preferences.
Good luck.