There must be already 12 threads about cydia issues.
Yes, the JB just came out. Yes there's millions of users JB, upgrading and setting up their idevices and just like every time there's a new JB cydias servers and all popular repos are getting slammed with traffic and most of the times dont respond to requests, you cant download or install anything or most times nothing will even show up listed.
Get used to it, have patience, wait a few days or a week, try installing your stuff at odd hours when thousands of users are not on or something.
There's nothing wrong with your iphone or cydia or your jb or your internet connection or your neighbors wifi or anything that has to do with the Mayan calendar