I've been compiling a list of unusual sources (i.e. not places where you expect them like PRONOM or libmagic) of file format signatures.
E.g. mime type applications often have them ("magic number" is one of the fields in the application template). Here is an example - http://www.iana.org/assignments/media-types/application/vnd.olpc-sugar
Often software applications that aren't focused on file type identification also have their own lists of format signatures.
E.g. ClamAV has a pretty good set: https://github.com/vrtadmin/clamav-devel/blob/master/libclamav/filetypes_int.h
Camlistore (a software project worth a look if you haven't seen it already) also has one: https://github.com/bradfitz/camlistore/blob/master/pkg/magic/magic.go
SQLite has an application_id pragma for applications that use it as a file format container to declare themselves. The SQLite source has a list of these: http://www.sqlite.org/src/artifact?ci=trunk&filename=magic.txt
Are there any other strange places where you've found a set of file format signatures?