During an Active Directory Upgrade project, I have collected many links and reference articles around upgrading Active Directory from Windows Server 2003 R2 to Windows Server 2008 R2. Since these types of projects have now been around for awhile, there have been many lists compiled by Microsoft professionals collecting this information. Therefore, this is only a collection of those findings and another reference to those that did the initial hard work for us all! The first link is the most comprehensive collection from internal discussion throughout Microsoft internal DLs.
Keep in mind, that before you dive into these links and articles, support professionals should do their due diligence of checking event errors and logs first, as many of these will reference some of those known Event IDs. Sometimes I would search the entire string of the error message to find related posts on other forums of Blogs on BING!
Another related Blog post from this project was Comparing Windows Server 2008 R2 Server and Core Roles and Features, as the customer wanted a side-by-side listing of what you might not gain if you only installed Server Core versus a full installation.
TARGET /Support Level
PRE/POST UPGRADE L1/2/3
W2K3 to W2K8 and W2K8R2 Active Directory Upgrade Issues
A large collection from Microsoft internal DL discussions. One of the most complete lists!
POST UPGRADE L1/2
Some of the 2008/R2 AD Upgrade Compatibility Issues
Short List of known issues
POST AD UPGRADE L3
Migrate Server Roles to Windows Server 2008 R2
After AD is upgraded, resources for migrating specific roles
POST UPGRADE L2/3
Description of Microsoft Server Applications supported on Windows Server 2008
PRE UPGRADE L3
How to Delete DLT Objects
In cases where are large number of DLT objects have been found, this will help to clean this up before a migration
Migrate Stand Alone Root CA 2003 to 2008R2
Issues and a link
DC Strict Replication Mode
May halt AD replication for up to 12 hours
Event ID 1388 or 1988 – Lingering Object Detected
Use Repadmin to remove
Application Servers Fail to Authenticate
Tips from MSIT