We just did a conversion from SQL Server 2000 SP4 32 bit to SQL Server 2005 64 bit SP2 9.0.3042.0. We have 16G of memory on the new box as well.
We had no CPU/memory issues on the 32 bit box.
We simply did a backup and reimport into SQL Server 2005. After a few hours, we noticed the 100% cpu (and the memory used was about 15.2G), so we rebuilt all the indexes on all databases/tables (used this script http://blogs.digineer.com/blogs/larar/archive/2007/07/30/smart-index-defragmentation-for-an-online-world.aspx)
Is there something else we need to do? I can't imagine this is due to bad queries since we didn't have the problem in 2000 (unless these bad queries were ok in 2005).
I know most of the db's are still running in 2000 compatibility mode as well, not sure if that matters.