You can use the dd command to make a bit-perfect clone of a drive. It's a command line tool that ships with OS X. In order to make the clone perfect you'll need to ensure the source and the destination aren't actively in use.
To prepare for the clone I recommend creating a secondary boot disk that you can boot from. Your source for the clone should be an offline volume, not in use, when you're making the copy. Otherwise you risk copying things that are in incomplete states on disk.
With your machine booted to your secondary boot disk, log in and fire up a Terminal or iTerm window.
Run diskutil to get a list of your available drives. One of them will be your target drive you're trying to clone. The other will be your source drive. For example:
> diskutil list
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *320.1 GB disk0
1: EFI 209.7 MB disk0s1
2: Apple_HFS Macintosh HD 319.2 GB disk0s2
3: Apple_Boot Recovery HD 650.0 MB disk0s3
/dev/disk1
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk1
1: EFI 209.7 MB disk1s1
2: Apple_HFS Backup 499.8 GB disk1s2
/dev/disk2
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk2
1: EFI 209.7 MB disk2s1
2: Apple_HFS Clone 499.8 GB disk2s2
Let's say that Macintosh HD (disk0) is the source and Clone (disk2) is the target for our dd operation. Start the clone with:
> sudo dd if=/dev/rdisk0 of=/dev/rdisk2 bs=1m conv=noerror,sync
When dd finishes you may see an error like this:
dd: /dev/rdisk2: short write on character device
dd: /dev/rdisk2: Input/output error
3726+1 records in
3726+1 records out
500107862016 bytes transferred in 14584.393113 secs (34290619 bytes/sec)
That last error message is actually okay. The last block written was a short block because there wasn't a full 1MB block to copy. No worries.
Now you've got a bit-wise perfect clone of your Macintosh HD drive. Reboot your system using the Macintosh HD drive and enjoy your clone!
In Mountain Lion and greater, you can create multiple separate backup disks with Time Machine. Get an USB external HD for traveling, and use that to backup your Mac whilst on the road. When at home, you can do a backup to another HD, (USB or otherwise,) which stays there permanently. I take this external HD when I travel. It is wicked fast, and demonstrably rugged, as I have dropped it several times with no ill effects. You can also use this disk to make a CCC clone, if that is your preferred backup method.
Note: It is not a wise idea to have a backup partition, (CCC, TM or otherwise,) on the same drive you're backing up. If the HD itself goes poof, you've lost the backups you need to restore your system.
Best Answer
Look into finding a copy of Winclone. The main problem for SuperDuper and CCC is the inability to write to NTFS volumes. They can backup your files, but often not necessarily capture the extended attributes with regards to ownership and permissions etc, resulting in an inability to make a sensible restore.
Winclone is no longer in active development, but it is effectively CCC for windows/bootcamp partitions. I've used it to transfer bootcamp partitions from one drive to another in the past.