aakk9999 - 10:14 am on Sep 4, 2013 (gmt 0)
Welcome to WebmasterWorld, sdgit!
Geo-targeting by subdirectory is pretty standard practice and easily set up. It only works if the main domain is gTLD, which, from your example, yours seem to be. I have used this techinque on a number of sites with no problems whatsoever.
What you need to do is go to WMT of your example.com site and add each subdomain as a "separate" site. I.e. you go and "Add a new site" and then in the URL name you type example.com/uk/ for the UK folder or example.com/au/ for Australia folder and so on.
Once you add folders in this way to WMT, go to manage each of these folder-based "websites" and set up geo-targeting for each as you wish.
Subdomains are possible but they prefer subdirectories because they pass authority to the root domain.
Yes, this is my experience too.
Will penalties to subdirectories strongly affect the whole domain?
They may or they may not, depending on the penalty. I think that from this perspective, the subdirectory is just a "page" on the domain. I have not heard of a site penalised based on "one directory", e.g. situation where "all URLs with /au/ are penalised".
But obviously, if the domain is penalised, it will affect all subfolders.