I remember Dean telling her, "I'll call you" and as he left, she mumbled to herself, "No you won't.."
I believe the writers wrote her out of the story, hence why she didn't appear in Season 3 and Season 4. The actress said the producers wanted Jo to be a love interest for Dean, but the general public perceived her as a "younger sister" figure rather than a love interest. The producers haven't made any decisions as to whether or not Jo will come back, but the actress has definitely shown interest and willingness to return.
Personally I'm a bit disappointed, I liked Jo and I wish they kept her for the continuing seasons.
Supernatural Wiki - http://en.wikipedia.org/wiki/Minor_characters_from_Supernatural#Joanna_Beth_Harvelle