I have several sites that I upgraded recently to 3.5. All with different customized (and vastly different) themes and plugins. One client contacted me to tell me that their back-end jQuery was no longer working: no fly-out, clicking on anything that would bring up modal windows would go to a new window, and most notably, they couldn't drag and drop any of the widgets anymore.
After just a little bit of troubleshooting this morning, I found the issue: in all the sites that had this problem, I had been calling in Google's API for jQuery (instead of using the WordPress native jQuery), and it was calling on an older version of Google's scripts. As soon as I removed that call (or redid the call to Google to the most current version of Google's API), everything worked just fine again.
I just thought I'd share this, because I saw there were a LOT of people having this same issue, but with no solutions. (I went through about 2 pages of this exact issue on the forum, but not one with a helpful answer.) So it could be a plugin calling in an old version of jQuery, or something in your theme calling in an old version through some method that *doesn't* just enqueue jquery. Whatever it may be, I thought I'd post my solution in case it would help someone else.