@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.
In TFS 11 we don't make use of the Excel workbooks anymore because we have the backlog and the board on the web. If you want to learn more about these features, you can check out the session by Aaron Bjork: http://channel9.msdn.com/Events/BUILD/BUILD2011/TOOL-793T
We have not really changed the reports in TFS 11. The reports you have will continue to work.
Feel free to ping me for more questions at ewald_dot_hofman_at_microsoft_dot_com