Carbon Copy Cloner will clone the Recovery partition (if that's what you want) when you are cloning the main partition, SuperDuper will not. So far that is what has already been stated by other posters. I have found slightly annoyingly that CCC when it clones the Recovery partition does so to a new one of 1GB in size whereas the original Apple one is only 650MB in size.
I was not aware Disk Utility copied the recovery partition but I knew it was possible to put multiple 'partitions' in to a disk image file.
However getting more on topic which is upgrading recovery partitions and/or installing one if it is missing. The solution I use for this is Create Recovery Partition Installer.
See https://github.com/MagerValp/Create-Recovery-Partition-Installer
This takes the Lion, Mountain Lion or Mavericks installers that you downloaded from the App Store and uses it to build an Apple installer package. This package when run by Apple's Installer program will then let you install the version of Recovery partition that matches the version of OS X you built the package from. I have therefore used this tool to make installer packages for Recovery partitions matching 10.7.5, 10.8.5, 10.9.1 and 10.9.2.
I can easily install any of these versions and even should I wish downgrade the installed version as well as upgrading the installed version.
You can obviously have a Recovery partition of say 10.7.5 and a boot partition which is 10.8.5 but the reverse is also true. I say obviously because the whole issue has been how do you upgrade the Recovery partition presumably to match the version of your presumably up-to-date boot partition.
As a reminder, yes you can have a recovery partition on a drive being used for Boot Camp i.e. Windows, no you cannot have a recovery partition on a drive that is configured as part of a software RAID set, yes you absolutely must have a recovery partition if you want to use FileVault2. You can have a recovery partition on a drive which has no OS X partition on it. The drive must be partitioned using the GUID scheme.
To completely cover the topic of Recovery partitions, DeployStudio now uses the Recover partition to build the NetBoot disk image you use with DeployStudio. If you are running DeployStudio on a server which is using software RAID then this does create a very annoying problem. You either have to not use software RAID on your server, or create the NetBoot set using DeployStudio Assistant on a second (non RAIDed) Mac, or when I last hit this I did find accidently that having another external drive plugged in which had a Recovery partition on it got round the problem.
Note: DeployStudio will restore Recovery partitions along with the boot partition for you to the Macs you are imaging.
If rather than using a 'monolithic' disk image with DeployStudio you use a 'thin' one created using InstaDMG or AutoDMG then there is no Recovery partition for DeployStudio to restore, fortunately these thin images are built in a way that automatically installs one for you.
AutoDMG is another tool by the author of Create Recovery Partition Installer.