I have written a small C program to take two file and compute the standard deviation of the difference of the two files. This operation is used for computing read noise from 2 BIAS frames, or dark noise from 2 DARK frames.
The program accepts files in PGM format. The DCRAW program can be used to convert from CR2 files to PGM with this command line:
dcrawMS.exe -D -o 0 -4 -v
The binary version of dcrawMS I use is from http://www.insflug.org/raw/Downloads/.
UPDATE 2010-08-26 I have included a version of dcraw I compiled with Tiny C Compiler which you can try before downloading dcrawMS.
Here is the Version 1.11 distribution for the calc_stddev program. It was compiled with the Tiny C Compiler and the source is included.
Once you have two different files converted to PGM format, you just use the program this way:
calc_stddev {File 1} {File2}