Not really an upgrade, but in 2009 on our first mother/son trip, the Front Desk Manager came to our room after we had checked in and handed us an envelope. Before we opened it, he wanted to explain that he was so touched by our story that he arranged a 'gift' for us.
We got into a conversation with him during check-in and spent 30 min together. Tim had mention how it was we came to be at WDW on this trip. He had been adopted at birth, but we were reunited in 2004 and have become very close since. Though I have been many times, this was his first ever trip to WDW - and it was to celebrate his 43rd birthday. There is a lot more to the story, but apparently he was just touched by our relationship and wanted to do something special for us.
He had arranged for a Segway Tour at Epcot - free of charge - and also for a taxi to insure we arrived early enough. Now, to me, that was way better than any upgrade and we have never forgotten him!
By the way, the picture of us below was taken on the day we were first united face-to-face.