If it is important for performance for an application to use one only
processor in HT, then the software vendor should provide a program option to
set this.
There are few programs that do not benefit from HT. For dual core, I
wouldn't worry about it. Server class programs EQ MS SQL Server 2000 works
better on 1 HT processor - you can set processor affinity in Enterprise
Manager. Other server class software should provide similar functionality -
ask the vendor.
If it is important from a s/w license perspective, then ask the vendor.
If the s/w is buggy on SMP, then submit bug reports to the vendor
Consider moving the process to single CPU system.
You can always switch off HT. With a SMP system, a good reason would be
needed.
If the reason has not been covered, then what is the reason?
http://tibit.com/technote/sbsmp.html
The above article is a bit specific, but the utility the author wrote may be
worthwhile.