The GNU Free Documentation License (GFDL). It's generally well-intentioned, but it places some weird restrictions on modification and reuse. In particular, it allows the author of a text to define "invariant" sections of a text which cannot be removed or altered in copies of the work, and automatically applies this restriction to sections of a document with certain names (like "Dedication").
The GFDL also theoretically forbids users from storing GFDL-licensed documents on encrypted storage, as the license states that "You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute". I don't think that reading was intended, but the license doesn't clarify further. :)
I'm curious about this, do you know which ones?