Noise generated using LT1026
You have output filtering on all the rails except the only ones that really matter (+- 9V), LC filtering in and out of the flying cap part will help, but I would replace it with something that does not do huge and completely uncontrolled di/dt.

Flying cap converters are evil from a noise perspective, far more so then something like a simple forward converter with a centre tapped transformer and a couple of fast diodes. 

I see that you are using non syncronous switchers, of the fairly low frequency sort with no synchronisation, personally I would replace the lot with some more modern parts up in the MHz switching region, and connect the sync pins,  much easier to filter. On the subject of buck converters, you have no real filtering on the input side so I would not be surprised to see plenty of switching hash on the input rail, and that LM317 has little input ripple rejection up there... 

Why even do the +9V with the flying cap? You only need 10mA or so, so what is wrong with a 78L09, LM317 or such? The negative rail could be generated by making one of the switcher inductors a coupled part, crude, but good enough and still better then that switched cap thing (Nope, don't like them).

Layout is everything with this stuff, so we need to see your PCB, including (critically) the ground plane and the bits around the power conversion stuff.