Annotations such as notes and links belong to the most appreciated PDF features. Although they are easy to use from a user's perspective this is certainly not true from a developers perspective since it is often not clear how to render them.
Each PDF file starts with a header comment that carries version numbers. What do they mean? Can a reader ignore these numbers or what is it to do? Is there any other version information that a reader should take care of?
Linearization is a feature to optimize PDF files for sequential reading. Although it is very useful in web based applications it interferes with other features such as digital signatures.