How to clone an entire disk with Lion (+Rescue) & Bootcamp Partitions
I know this is not a fully integrated solution, but you can use the tools available on Mac OS X and on the Mac OS install DVD/FlashDrive. You will have to restore both systems separately, but it will save you from having to reinstall everything in Windows and OS X.



Note: If your drive is phisically damaged you might end up with corrupted data or being unable to clone your partitions.



There is a thread here explaining how you can save and restore your Bootcamp partition using only Disk utility and BootCamp: http://forums.macrumors.com/showthread.php?t=997823

It goes along the lines of (parts are just copied):


Use Disk Utility to backup your bootcamp partition to an external drive.
You can also use Disk Utility to backup your Mac OS partition if you didn't use Time Machine.
Install/Restore Mac OS to a new Hard Drive
Use Bootcamp to setup your drive for windows and to allocate the new space.
Use Disk Utility to restore your .dmg image to the new Boot Camp partition you just created. Be sure to run IMAGES --> SCAN IMAGE FOR RESTORE in Disk Utility before restoring. You may need to unmount the Boot Camp partition in Disk Utility before it begins to restore.
Use fdisk in Terminal to mark the Boot Camp partition active. First, enter the fdisk MBR edit mode by running the following:

$sudo fdisk -e /dev/disk0


Ignore the error "could not open MBR file /usr/standalone/i386/boot0: No such file or directory". Then, determine which partition number to mark active by running the following (in bold):

fdisk: 1&gt; show


Your windows partition should be #3 labeled "Win95 FAT-32". Now, mark the partition active:

fdisk: 1&gt; flag 3
Partition 3 marked active.
fdisk:*1&gt; write
Device could not be accessed exclusively.
A reboot will be needed for changes to take effect. OK? [n] y
Writing MBR at offset 0.
fdisk: 1&gt; exit


Now, reboot and hold the OPTION key and Windows should be listed as a bootable option."