After you upgrade to SQL Server 2008, you will also need to update these assemblies to the .NET Framework 3.5 SP1 version ...

After you upgrade to SQL Server 2008, you will also need to update these assemblies to the .NET Framework 3.5 SP1 version using the ALTER ASSEMBLY statement. SQL Server 2008 does not automatically use .NET Framework 3.5 SP1 assemblies from the global assembly cache (GAC) or automatically update these assemblies in the database since it could cause data corruption of any persisted data dependent on these assemblies. SQL Server 2008 CLR integration requires .NET Framework 3.5 SP1 version assemblies. SQL Server 2008 CLR integration will generate an error if you use the .NET Framework 2.0 version of these assemblies 
 
More details can be found in the Microsoft Knowledge Base article 949080