I’ve created a small bash script that works in combination with the command-line version of PhotoFlow, initially with the idea of automating a superresolution technique described in this same forum (see this post and the link to the script).
However, the same can I think be used to increase the SNR by combining several similar images, if no up-scaling is performed. It could be combined with 32-bit floating point TIFF output for best results.
The script works on RAW input images, and calls align_image_stack to align handheld shots prior to the averaging step.