Let's start a list...
...of things we know are optimized for SMT. I'm willing to bet any hypervisor is. That means KVM, VirtualBox, Xen, and VMWare. I am almost positive that gcc would be on the list.
What about:
Python?
Java?
HTTP servers?
Databases?
Please add a reply if you know for sure about anything that is optimized for SMT so people can be ready if needs be.