Hi Rachael!
You are going to have a fun-filled 3 days! First of all, you can't see everything at Disney World if you were there for 30 days! So, don't worry about trying to see it all.
If I had 3 days with my 3 year old, I'd do 3 parks. I'd do Magic Kingdom first, then Animal Kingdom and probably Hollywood Studios after that.
I'd pick out the 3 or 4 most important attractions to see and make sure those get done (by getting a Fast Pass, etc.) and then whatever else you get done at the park will be frosting!
At Magic Kingdom I'd make sure to do Dumbo, Mickey's Philharmagic, Small World and Country Bears AND the parade or any special shows!
At Animal Kingdom you'll want to see The Festival of the Lion King, Finding Nemo The Musical, The Boneyard, The Kilimanjaro Safari and the Jungle Trek and Expedition. And the parade, too!
At Hollywood Studios, your 3 year old MUST see Disney Jr. LIVE, Muppets 3D and all the Pixar Meet and Greets!
Hope that helps! Make sure you check out the
Traveling with Little Ones section of the site, there's tons of good info and a printable kid-friendly map of the parks!