Protected E-mail Headers (Enigmail)
Enigmail allows the encryption of the subject line, References, etc. for
PGP/MIME-Messages (The orginal subject line becomes part of the encrypted
MIME-part). This feature is already build in an can be enabled by setting the following options in Thunderbird's about:config.
extensions.enigmail.protectHeaders trueProtect sensitive headers of encrypted messages, such as the subject. The original header is moved into the encrypted message and replaced by a dummy value (such as "Encrypted Message"). This is part of the Memory Hole standard that is currently being developed.
extensions.enigmail.protectedSubjectText Encrypted MessageText to use as replacement for the subject, following the Memory Hole standard. If nothing is defined, then "Encrypted Message" is used.  (Remark: if not set, "Encrypted Message" might be translated)
This feature is not unique to Enigmmail and has been implemented to other platforms but unfortunately it's not that wide-spread  either. That means, that in the worst case, the other side will just see "Encrypted Message" as subject line---but that seems to me a rather small trade-off.