Can I throttle individual databases instances on one SQL Server 2005 box
You could use the Windows System Resource Manager (WSRM) feature for this.
It is not present in Windows starting from 2012 R2, but since this is an old SQL 2005, I would expect the OS to be old-ish as well.

I've never used it myself, but, though a bit complicated, it might do the trick for you.