What doesn't get cloned to new hard drive in Super Duper? I recently upgraded my 2010 Macbook Pro HDD to an SSD. I went from a 500GB HDD to a 512GB SSD (Crucial M4). I formatted the new SSD using Disk Utility into Mac OS X Journaled file system. I then used Super Duper to clone the original drive over by selecting "Backup -  all files" from the dropdown.

I recall that the original drive had about 120GB of free space leftover on it. With my newly cloned drive, it states that there's 195GB free. I primarily used iStat Menus, to measure the amount of free space.

So the math looks to be like:

195 - 12 - 120 = 63

About 63GB of difference, taking into account the 12GB of increased storage already. It's actually probably closer to 70GB considering I've added some new files in usage recently. 

What didn't get cloned over to the new drive in this approximate 60-70GB? 

Everything boots up and runs just fine. There just seems to be some kind of discrepancy of what was reported as free before and currently.

Some things to consider:


I have Windows 7 (Ultimate) and Windows 8 (Preview edition) as VMs using Parallels 8, which were cloned over.
This is taking into account that I emptied the Trash already.
The original HDD is a Seagate from Apple.
When you select the SuperDuper script / copy mode, you can change the scripts, that SuperDuper will run during the copy process.



As you can see, a couple of files are omitted:


So the temporary and cache files, etc. may have taken quite some space on your old disk. Some other possible reasons could be:


SuperDuper omits OSX swap files (/private/var/vm), which can become quite large
The spotlight index is rebuilt after cloning a drive. Depending on your system, the spotlight index may become quite large as well over time.
SuperDuper does a permission repair before cloning. Maybe some space was liberated on your old drive during that process.
As Richard suggested, SuperDuper does not clone the hidden rescue partition. But this should not be more than ca. 1GB