Well. As long as the OS handles them properly then you will gain performance simply by the os doing 2 things at once. The OS might use one core to handle it's own functions while the other core is used for an application, for example. Servers have been doing that kind of thing for years, so even if the particular app won't take full advantage of it, you still will gain a bit of improvement, especially if you are multitasking and each app uses a different core.
I believe stuff like Maya, 3D studio Max, CAD, and Adobe's Production studio (Premiere, After Effects, Encore, Photoshop etc) are truly multi threaded. I've seen 80% performance increase going from single core to dual core cpus.