It really depends on which type of trail running shoe you're looking at. For example, something really low-profile like some of the Inov-8 shoes or the New balance MT-100 would not benefit from insoles. You'd be defeating the purpose of being low to the ground (READ: Stable) by adding the extra support.
However, higher volume trail running shoes with thicker heels are essentially the same thing as other running shoes and if insoles help you there, they should help again.
Superfeet do control pronation, so if you're a neutral runner you may want to forego them and let nature provide you all the ankle support you need.
If you have higher arches, like I do, there are other options for support that don't interfere as much with pronation. I like Arch Molds, as they are more flexible than Superfeet and do less to interfere with my neutral gait. However, I do not use them in my Inov-8 shoes but do use them in more substantial shoes like the La Sportiva Wildcat and in my heavier boots (right now, Salomon Quest 4D). They mold to your feet after a couple of runs (or hikes) and provide just the right amount of arch support without being so stiff that you can't feel the trail.
Like was mentioned above, your best bet is to have your gait analyzed and let a pro fit you. Good fit and proper shoe design can really help eliminate many of the problems we encounter with our lower extremities.