Partitions don't really have free/used space, filesystems do. If your imaging tool recognizes and has support for a given filesystem, then it can resize.
I am pretty sure clonezilla has at least ext*, fat, and ntfs resize support.
See the expert resize option.
http://clonezilla.org/clonezilla-live/doc/03_Disk_to_disk_clone/advanced/05-advanced-param.php