When I was deciding on a motherboard for my Haswell rig, one of the things that I looked at was automatic fan controlling capabilities. I has a hardware fan controller bay but it was automatic. And it was a cable hell. Asus boards were on top of that chart with their "mature" Fan Xpert 2 software. So I settled for the Asus Maximus VI Hero motherboard.
Since then I had been using the Fan Xpert 2 software to control the fans of my PC. It currently controls the two CPU fans, 180mm two bottom intakes, 120mm top exhaust and 120mm back intake. (Yes, it's a weird fan setup but that's by Silverstone Raven RV03 case's design).
Anyways, one of the cool feature of this software is that it can completely turn off the case fans when the CPU temps are low enough. (Basically when the CPU is idling.) But it doesn't turn off the CPU fans completely. Must be a safely feature.
I think this feature is causing the dust to pile up inside the case. Basically, when the case fans are not running, the airflow inside the case is governed by the CPU fans and the GPU fans. Since the positive air pressure is not maintained (by making intake fans' CFM > exhaust fans' CFM) this causes air to sneak in from places that you don't want them to sneak in from. Air doesn't just come in alone - it comes with dust. Dust doesn't come in from the holes where intake fans are installed because they are properly filtered. It's the other gaps in the chassis that let the dust in. There is no way to prevent dust from sneaking in through those gaps except for creating a positive air pressure.
So I've changed how the Fan Xpert 2 controls the fan speeds. I don't let the intakes completely come to a halt anymore. I can stop the top exhaust fan completely because it is an exhaust fan.You can see the fan speed graphs in the following two screenshots. (click on the images for a clearer, larger image)
I should have cleaned the case internals but it is a tedious thing to do. I don't have time nor the motivation. Plus, I don't want to arouse the dust inside the apartment because of the baby. At least now the dust problem will be controlled. I will probably clean up the internals next time I upgrade some component inside the case. But it isn't happening in the foreseeable future.