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 is the source and Clone is the target for our dd operation. Start the clone with:
> sudo dd if=/dev/disk0 of=/dev/disk2 bs=128m conv=noerror,sync
When dd finishes you may see an error like this:
dd: /dev/disk2: short write on character device
dd: /dev/disk2: 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 128MB 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!
Edit: To address a slowness comment made by @Gordon Davisson in his answer, there's some anecdotal evidence out there that using rdisk# instead of disk# can make dd a whole lot faster. I haven't tried it though. So your dd call would be:
> sudo dd if=/dev/rdisk0 of=/dev/rdisk2 bs=128m conv=noerror,sync
in the above example.