I'm a huge fan of using EXIF and IPTC embedded metadata in images, and I know, that only a few pieces of software, used for stacking and image manipulation are capable to keep (or write) EXIF sections into resulting images.
Just in case if someone wants to be able to do some tricks with EXIF, I'd like to briefly share my own techniques.
First tool I'm using to manipulate EXIF is JHead. It's not GUI software - you have to run it from command prompt. It's cross-platform, so you can use it everywhere from Windows to Linux.
Official website: http://www.sentex.net/~mwandel/jhead/
It's not a "Swiss army knife", but it does quite a bit. For example, to transfer the whole metadata section from one file to another, you have to run this:
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jhead -te donor.jpg recipient.jpg
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jhead -purejpg yourphoto.jpg
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jhead -ft yourphoto.jpg