It's always a nice surprise to arrive in Disney and find out you've been upgraded free of charge. There seems to be no pattern to Disney sprinkling a little pixie dust on your vacation, but it happens on a fairly regular basis.
Some upgrades are small like a water view instead of a woods view. This happened to my family in August 2004 when Hurricane Charlie forced us to drive instead of fly because the airport terminal was damaged and no flights were going in or out for days. We had booked a "woods view" at the Wilderness Lodge. We called the resort to let them know that because of the hurricane, we'd be driving and arriving very late. We were given a room with a view of Bay Lake, overlooking the dock where the boat picks you up for the Magic Kingdom. My guess is Disney wanted to add a little magic to a trip that was starting out on the wrong foot.
In December I booked a package with a room at Animal Kingdom Lodge. The Savannah view rooms (where you can watch the animals from your balcony) were not available when I booked. So I booked a standard view room. Our flight arrived early in the morning and our room wasn't ready when we arrived. We got our park passes and were told to come back at 3 p.m. and our room would be ready. When we returned, we had a room overlooking the Savannah. Now these are nice little surprises! But I've heard talk about upgrades at deluxe hotels that include being upgraded to concierge or club level. I've also heard about upgrades from value resorts to deluxe resorts, though they appear to be a little more rare.
The only advice I have on upping your chances for a free upgrade, is letting Disney know (when you make your reservation) if you or anyone in your family is celebrating anything while there, such as a birthday, anniversary or graduation.