For some, re-installation of individual programs is not an option - for example, when the original media can't be found.

There are two ways that I know of to get around the "mess" than results from drive cloning to a new machine.

1) Do a windows backup, install windows on the new machine, then restore from the backup.
2) Clone as described, then do an upgrade install of Windows.

Either way, you DO need Windows media and license keys. #2 is also a decent way to move from a physical to a virtual machine.

Note: if you're moving to a different CPU type as defined by Microsoft, you have to do a windows reinstall of some sort. Basically, changing between Intel and AMD, single vs multiprocessor, ACPI type (devices->computer), etc.,will not work without a re-installation of some sort.