I had the same problem after updating to Mavericks. Both Xcode 4.6.3. and Xcode 3.2.6 were hanginig endlessly during "Creating Universal Binary."
As it's the lipo
command line tool that's creating the universal binaries I did some research and found this discussion which solved my problems:
Installing psycopg2 has it stuck between xcrun and lipo
According to the answers given there Xcode apparently didn't find lipo
in the end but unfortunately shows no error message in this case.
After backing up the 10.9 version of /usr/bin/lipo
and linking in /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin/lipo
as described in the post creating the universal binaries was working again.