The builders of an FDR must comply with [DO-178C][1] ([DO-178B][2] may also be of interest here) as per [AC 20-141B issued by the FAA][3]. These documents do not specifically define a data format but provide requirements for what it must be resilient against. Here is an [interesting research paper][4] that covers some of the topics you are asking about. Since most avionics use [ARNIC 429][5] as their standard of communication some FDRs provide [ARNIC 429 inputs][6] to record the avionics instructions at the time. I would assume these inputs dump the bus data right to the storage medium (most likely solid state memory these days). Since the formats the device uses may be proprietary as well as very low level (and memory efficient) I am sure they make software to dump it to other formats. For example [L3 makes a full unit for their FDRs][7].

It should also be noted although they may have all been phased out by now, some older cockpit voice recorders and FDRs recorded on analog mediums and may still be inservice doing so.  


  [1]: https://en.wikipedia.org/wiki/DO-178C
  [2]: https://en.wikipedia.org/wiki/DO-178B
  [3]: http://www.faa.gov/documentLibrary/media/Advisory_Circular/AC%2020-141B.pdf
  [4]: https://people.cs.uchicago.edu/~shanlu/paper/FDR-OSDI-CR-FINAL.pdf
  [5]: https://en.wikipedia.org/wiki/ARINC_429
  [6]: http://www.l-3ar.com/pdf/datasheets/MKT060-AP_DASU_12-12rev3.pdf
  [7]: http://www.l-3ar.com/pdf/datasheets/MKT064-AP_RAU_12-12rev3.pdf