Mostly just that Disconnect is open-source, and isn't backed by a media & analytics company (Evidon Inc.).

Some find it to be more transparent, and in many ways it is, but really you won't see much of a difference between the function of the two. I personally use Disconnect, and have yet to find it break any sites. I find setting Flash to ask before being enabled on web pages tends to break more sites than anything else.

The major different for me is the privacy concerns around Ghostery. http://lifehacker.com/ad-blocking-extension-ghostery-actuall...