@Allen Feinberg: In the upgrade from TFS2008 to TFS2010 there were major changes in the query architecture. In this upgrade that is not the case. During upgrade we will not touch your queries. Anything you want to do with queries, you need to do yourself.
The same is for the linktypes. We will not do anything in this area. Custom link types will continue to work in an upgraded team project.
For the work item categories: I don't understand the question.
On custom controls: your controls for windows will continue to work but if you have created web controls, you need to redo them. There is great guidance from the rangers at http://vsartfsptguide.codeplex.com/ which includes how to create a new web control for work items.