I also shoot manual most of the time, but occasionally save something into C1/C2/C3 depending on the situation at the time. I do not have any standard/permanent settings saved.
Here are a couple of examples of how/why I might set them up....
1. I'm beside a lake and shooting birds both in flight and on the water. The light is steady and manual exposure is a fine choice. However, for BIF I will want AI Servo, maybe expanded AF points, a high shutter speed and a high ISO to match it. I may also want high FPS set for shooting bursts. For floaty birds I don't need AI Servo, and One Shot would be better, along with single point AF, a much slower shutter speed and reduced ISO to match. I can also probably be happy with single frame shooting, or maybe low speed continuous.
My exposure can still be set up for the identical lighting, but so many aspects of the camera configuration will need to be changed quickly. Nothing easier than flicking back and forth between C1 and C2. If the light changes then I can easily tweak and re=save the settings again or temporarily oveeride them, knowing that if I twiddle back and forth my original saved settings will be restored.
2. I'm on a woodland walkabout and the lighting is very variable between the trees, with sunlight peeping through in some places and a varying density of canopy. At times I find myself in a clearing with clear skies. For the clear skies I'll be set up for BIF, with manual exposure to avoid complications from the sky, and the camera set up to shoot action. Within the woodland I do not expect to shoot action, but with the lighting up and down I want AV mode and the rest of the settings much like those for floaty birds. However, in this instance I choose Auto ISO and partial metering to cover a much broader range of lighting conditions and to respond instantly to changes so that I can shoot quickly, before my prey has hidden.
Something else you could do, if you're a manual shooter, is to simply set up three combinations of exposure e.g. for shallow DOF, medium DOF and extended DOF, all while maintaining the same overall exposure. Then you've got just one click of a single knob to deal with instead of repeatedly having to twiddle two or three knobs by any number of clicks to keep things on the level.
Another option - save a setting for general purpose snapping, where you have no time to think about anything at all and just need to grab the shot fast. Stick it on P with Auto ISO and evaluative metering and the focusing however you like and leave the camera on that saved setting, ready for just about anything. Maybe stick that in C3.
The choice is yours. If you can't think of a use for them then ignore them. There are plenty of features of the camera which I ignore.