Cue began life as Greplin, and it was a personal assistant app that was sort of like Google Now, but without the Google Search features, and without the lock-in to Google Apps. Cue would aggregate social data from various services - Gmail, LinkedIn, Facebook, Twitter, Dropbox, etc - and build a daily plan for you. The idea was to offer you relevant information at the right time, including flight information or reservations.
The idea is that Apple is likely planning to integrate this sort of functionality into the new "Today" page in iOS 7's redesigned notification tray. It seems likely that some functionality would also make its way into Siri. No word on when this will happen, but this would be a pretty big addition to iOS, so we wouldn't expect to see it until iOS 8 comes out about one year from now.