Since Loot34 has dropped my name
VCM and VCMII are ford's official factory service agent J2534 passthrough programming devices. You can buy the hardware from the ford or motorcraft or possibly even from its manufacturer bosch. The windows software component is ford's IDS for which you can buy a license.
The clones are of variable quality, from nearly useless through to fully functional. To date vcmii copies seem to be of much higher quality than the vcm copies. The software does not seem to be free of issues, my calibration disc is corrupt and the support from the supplier has been non existant - fortunately a member on here has a good disc
Also there are likely to be virus infections on some of the additional tools, my extended programming unlocker was infected. The biggest problem with software is that many web sources are on internet sites the apparently hold pirated software which british isps have been told to block, if you can't get around that then you might be best to leave the computers side of servicing a ford to you dealer.
The ordinary install of IDS does not enable "Module Programming" - if you want to install a new bcmii or update your pcm software you need to use the "extended programming" tool to enable the functionality. For information the dirty ( virus infected ) version that is about 250k in size and a clean version about 200k in size and antivirus tools will break the tool. This tool enables the module programming for 100 days, after it expires you run the tool again to get another 100 days. I have also found a modification to enable the functions for 1000 days but not used it yet.
Note this is for the IDS software, you can install ETIS after IDS so that the vehicle id can be read from a connected vehicle rather than having to enter the chassis number in ETIS yourself. Beyond that then unless the latest etis has changed a bit all it does is allow you to click on a link to start ids - which it usually calls wds.
Diagnostic software update files are sourced from the web but not through the ford etis gateway, in fact I've seen a suggestion that ford might try to disrupt unlicensed etis installs if updates are attempted from the official source. It is reported they took action to prevent the unlock from 2006/7 working with recent versions of the software form say 2013/14.
Vehicle software updates - calibration files - can be obtained for free provided you know the file name, there is no changelog that I can find yet so the changes from version to version are unknown. For example, if you pcm is 2008 vintage on an original calibration then you will not have anti stall but updating to the latest will add the anti stall function, but there is no list to tell you that. Also calibrations are quite vehicle specific being related to at least engine size, power and axle ratio.
Sorry for the long post and don't be afraid to ask questions.