The pop-up maneuver's goal is to minimize exposure to enemy fire. Imagine that you're flying an F-16 over enemy territory and that you want to hit a nuclear power-plant with a couple of JDAM's. Since the target is certainly protected by lots of AAA and SAM's, you want to drop the bombs as far away as possible from the target. In other words, you definitely do not want to fly over the target, as that will most likely get you shot down.

You can use the pop-up maneuver then. You fly low and fast to avoid radar detection and AAA fire. When you get close to the target you climb at 45 degrees, roll 180 degrees (you are now flying inverted), prepare the JDAM's to be deployed. You then pitch up and when you are at the top of a parabolic flight path, you release the JDAM's. The inertia build-up during the ascent will make the bombs go faster and farther. Once the bombs are deployed, you fly low again.

There are some technical papers on this. It's heavy math: optimizing flight paths is not exactly a trivial problem ;-)