The Indiana Jones Stunt Spectacular is open. The Backlot tour is closed until April because they are working on the new Stunt Show Attraction that will open in 2005 in Disney MGM Studios.
Yes, Alien Encounter is closed, so they can incorporate Stitch into a new attraction.
The Wonders of Life Pavillion at Epcot will only be open seasonally, and Food Rocks in the Land Pavillion is closed to make way for the new Soaring Over California attraction to also open next year.
Periodically, other attractions close for a few weeks at a time to allow for annual maintainance and rehab.
I don't think you will find too many attractions closed, as most big rehabs have already taken place. You can call or go online to check before you get there to avoid any disappointments.
Have a great trip!