Change your command line to;
C:\Software\Android\APK\keytools\key>C:\"Program Files (x86)"\Java\jdk1.6.0_16\bin\jarsigner -verbose -keystore kill-them-all.keystore -signed jar kill-them-all_signed.apk kill-them-all.apk kill-them-all.store
You should just give the name to the key store, not the full path.
/Fredrik