Do you have a specific microcontroller you want to use, or have experience in? Do you have a $ amount you want to stay under? Is this going to be for a production unit, or one off?
There are devel boards out there for many uC's that already have SD or even CompactFlash connectors with sample software. It would be just a matter of connecting the 12bit AtoD converters of you choice to the devel board.
I'm thinking of the ARM ones right now, since there is a nice FAT file system libraries for free available, which would allow you to just pull the card and read it in a PC. Something like:
https://www.olimex.com/dev/sam7-p64.html
Otherwise, if you want to go cheaper, I'm sure a quick google search will find devel boards for AVR or PIC with SD connectors on board.