Hi,
Unless you have changed any vCenter Server configuration as per your environment or as per vendor recommendation, its best to set-up a new database and re-register the hosts with the new vCenter Server.
I too am in the process of migrating vSphere 4.1 to vSphere 5.1 and the vendor recommended to proceed with fresh installation.
The reason they told for fresh installation is that if there was any DB inconsistency, it will be eliminated.
My environment - Windows 2008 R2 Enterprise, SQL 2008 Enterprise, two vCenter 5.1 Servers and around 50 ESXi 5.1 hosts.