DC/DC converter with 12 outputs, low noise?
You could do a flyback with multiple outputs.  

You can wind multiple output windings and a single primary to get a bunch of 6V outputs followed by an LDO on each.  The regulation of the non-regulated outputs won't be great, but you don't care because you have LDOs on the output.  

Also, a flyback doesn't have great ripple performance so you need an LDO with good PSRR at your switching frequency.  You'll need very good LDOs.

Finally, I've never tried a 12 output flyback and it might be problematic from a transformer design viewpoint.  (Proximity effects, leakage inductance due to poor coupling, poor efficiency due to fringing and AC losses, etc.)  

You probably want to limit the secondary windings to 4, and use 3 flyback controllers.  You could experiment with more because your current is low.