There is a new feature in MDT 2012 RC1. It will keep the list of items (applications, drivers OS packages, task sequences) in alphabetical order.
Now when you first install MDT 2012 RC1, you might notice that the items aren’t sorted right away – you have to change something in the folder first. As soon as you do (e.g. add an item, rename an item), the items in that folder will be sorted.
Keeping the list of folders sorted is a much bigger challenge, so at this point they will still show up in the order that they were added.