Will you have park hopper tickets, or will you have to stay in one park all day? Do you expect to take mid-day breaks or stay in the parks all day?
I have a DD7 and a DD3. Here is what they love:
DD3 - the shy one - Fantasyland in MK, Playhouse Disney at MGM, character meals (Crystal Palace, Chef Mickey's, we're going the princess route next time, but you have boys), the fireworks at MK
DD7 - the thrill seeker - loves Splash Mountain, Space Mountain, Big Thunder Mountain Railroad, Tower of Terror (her favorite ride!), Kilimanjaro Safari, Fantasyland (Peter Pan, Mickey's Philharmagic), fireworks, character meals, Test Track, Soarin'
Next time we go, we will have to see the Nemo show at AK and the Nemo ride and Turtle Talk with Crush at Epcot. I also think DD3 will love the Little Mermaid show at MGM -she has not seen it yet, but her sister has.
Is this your first trip? We will have three full days after our cruise in January, but my kids have each been to WDW many times.
Here is our itinerary if it helps:
get off Disney Wonder Thursday am, go to MGM studios, lunch at Hollywood and Vine, Epcot in the afternoon/evening, Illuminations if we are still awake
Friday - MK, lunch at Crystal Palace, Bibbidi Bobbidi Boutique, dinner at 1900 Park Fare
Saturday - breakfast with Lilo and Stitch, then AK to see the Nemo show, ride Expedition Everest, see Festival of the Lion King (we do that every trip!).
It is too short of a trip for us, but it is worth it so we can do the cruise!
If you have never been, you might not want to try to do all four parks in three days. We are just hitting our favorites this trip since it is an add-on to the cruise, but we won't get to do everything we want to!
One other thought - if one of your half days is also a day for Mickey's Very Merry Christmas Party, you could get tickets to that and have fun there (it is at MK and is from 7-midnight). MK will close early on party nights, so you might pick another day for MK if you are not doing the party so you can maximize your park time.
One more thought - going in December, your boys would probably love the Christmas lights at MGM!
Hope this helps!