How to automatically rotate images based on EXIF data?

You may use the free jhead (which itself uses jpegtran).

To fix a picture named "image.jpg" just type :

jhead -autorot image.jpg

To fix all JPGs having EXIF data in the current folder use :

jhead -autorot *.jpg

If once rotated the thumbnail icons do not show correctly, you could refresh them by :

1. Create a new folder (keep the untitled name)
2. Move the affected images into the folder
3. Using Column View, move the images back into the original folder
4. Delete the empty untitled folder

You can use nconvert, which is freeware (for private and educational use) and available for Win, Linux and Mac.

This tool can rotate JPEG images lossless according to the EXIF orientation tag:

nconvert -jpegtrans exif -o 'rotated_%.jpg' *.jpg

That command will batch convert all JPEG files in the current directory and prepending their names with rotated_. This is controlled by the -o option, refer to nconvert -help for more possibilities:

-o filename       : Output filename
   Use # to specify position of numeric enumerator
   Use % to specify source filename
   Use $ to specify full source pathname
   Use $$ to specify source folder name