We were on 2008.3 and then went to 9.1 SP2. The upgrade meant we had to install the last service pack for 2008 and then install to 9.1 and then install the SP2 pack. This change fro 2008.3 to 9.1 SP2 was a big pain for us on the Reporting side. The MyServices and ServiceDesigner pieces had little problems. This was an upgrade from Win2003 w/ SQL 2005 to Win2003 w/SQL 2008. We've been running 9.1 SP2 on SQL2008 for a year now with no problems.
We are now upgrading to 9.3.2 and are just going to run the 9.3.2 installer. We will have new servers put in place with Win 2008R2 and on the database side have just done an inplace update from SQL 2008 to SQL 2008 R2. This means that currently we are running 9.1 SP2 on SQL 2008 R2 in production. We run a very high volume for RequestCenter so the setup works fine for us in this topology. Going to Win2008 we are going to copy the database tables and run an in-place upgrade on the newly built Win2008 app server.
As for CatalogDeployer, we kept the old environment and the new environment around while testing the upgrade. This meant we could make changes to Prod using the old environment and then once production was upgraded, we deleted the old environment.