Other suggestions are to validate the memory configuration and the disk alignment. I've posted this to #sqlhelp on Twitter.

OK. Stepping back for a minute. What kind of monitoring do you have in place? Can you see where the slow down is occurring based on the metrics?

Another option, can you capture a trace on the old server and then play it back on the new server? How does that perform?

Finally, I ran into a number of application side issues, in and around connections, when moving from 2000 to 2005. Same to 2008 from 2000. Has anyone examined the code to see what connection settings it's using are within best practices for 2008. Also, have you updated the connection DLLs since you're on a new version of SQL Server? It's possible the problem isn't on the server at all.