There is a known issue when cross-compiling for iOS on OSX:
http://sourceforge.net/mailarchive/message.php?msg_id=30462917
In short, you need to run
$ autoreconf -fiv
in the libjpeg-turbo directory before running configure.
On OSX 10.9 and Xcode 5, below are the versions of tools that you will need to compile the lib successfully. Newer versions will not work.
- autoconf 2.69
- nasm 2.08.01
- automake 1.13
Alternatively, you can just use the prebuilt binaries that comes with the DMG:
http://sourceforge.net/mailarchive/forum.php?thread_name=5255ABCE.8070705%40users.sourceforge.net&forum_name=libjpeg-turbo-users