On pocket pc's it has been my experience that CF cards and SD cards are both adequate. We have had problems sustaining 24/96 to CF cards, but I think this was largely due to the requirement of passing the data through a 16-bit PCMCIA interface to get the data to the storage device. (SoundDevice's recorders use CF cards.)
On newer machines we have used 150x SD media with excellent results.
How does the user preference of sampling rate, etc get passed from the mic A>D to application software?
In our case it was a question of transmission over SPDIF. You can auto-detect the rate from the SPDIF stream (SPDIF receiver chips can do that), or you can let the user set it to whatever they want and require that the transmission rate and SPDIF receiver's rate match. I made a design choice to implement both. The user can lock onto the sampling rate of the transmitting chip or set it to a specific rate. If the application is expecting a specific rate and it's something different you get an error.