I've been attempting to access your 2012 article, "EXIF Orientation Handling is a Ghetto", but it looks like your site is messed up. All of your URLs lead to pages of gibberish. I managed to find a Google Cache of your main page, but it also seems your articles are not cached.
A) I thought you should know, just in case you were unaware.
B) I'd still really like to get at that article, if possible.
Imagemagick has an option "auto-orient". This applies the inverse of the exif orientation to the image data, and then sets the exif orientation to "top-left" ie unrotated. However, it does not touch the exif thumbnails. This leads to an image with inconsistent orientation. The thumbnails in file managers etc will now be displayed with "top-left" orientation and so will appear incorrect, but opening the image in a viewer/editor will work correctly. Adding thumbnails to the images would allow to catch this edge case, and I expect that a lot of websites are using this feature of imagemagick.
Slightly off-topic, but I tried to look at the article on your website and it looks like something isn't working (confirmed on two different machines):
Thank you for your blog post, it finally put me on the right track.
Im afraid there was some mistake with sample images. They all seem to have orientation flag set 0
Am I confused or are most of these images missing the EXIF data? Landscape_1.jpg is fine, but all of the other Landscape images have no EXIF data at all. Same with the portrait images.