Its for non-image data that may be used by the camera when processing, storage for user settings (i.e. 1D series...maybe 5D as well), and from what I've heard, storage of temporary audio streams when recording video. Its kind of a catch-all folder that stores anything that doesn't belong in the DCIM folder, and I think most (if not all) of it is temporary data.

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Due to curiosity, I searched a little more research about canon folder structure. It seems like there is a fair amount of information that can be stored on a memory card by modern Canon cameras such as the 5D Mark II and 1D/s Mark III series. There is obviously the DCIM folder, however unique to Canon, you may also find a CANONMISC folder within the DCIM folder. This contains canon- and camera-specific information that allows the camera to manage the DCIM folder...such as thumbnail metadata for images saved in the camera-specific or stream-specific folders. Also under the DCIM folder will be camera or stream specific folders, such as xxxEOS1D or xxxCANON, where the xxx is a number (100-999) indicating the current photo stream. Images within each photo stream are numbered from 0001 through 9999.

At the same level as the DCIM folder is the MISC folder. This does indeed contain metadata, temporary files, as well as certain settings. Specifically, the MISC folder contains DPOF, or Digital Print Order Format, settings, used when you print directly from the camera to a printer.

The full Canon folder structure is as follows:

\DCIM
    \xxxEOS1D
    \xxxCANON
        \***YYYY.JPG
        \***YYYY.CR2 (raw photo)
        \***YYYY.MOV (video)
        \***YYYY.THM (thumbnail)
        \***YYYY.WAV (audio)
    \CANONMISC
        (DCIM control metadata)
\MISC
    (DPOF settings)
    (GPS data)
    (temporary data)