How can I tell Google that multiple domains are related?

This is a question that a website/domain owner sent to Google Webmasters:
“Is there any way Google identifies “sister” websites? For example, relationships between ebay.co.uk and ebay.com? Does linking from one to the other is taken as paid or unnatural? And I’m strictly talking about good, genuine ccTLDs for businesses :)”
Adeel, Manchester, UK

According to Matt Cutts there are 2 ways to do it:

1. Using an href link to point to the ccTLDs (that is the better way to do it) or;
2. Just make a site map with all the different ccTLDs

Of course all this only applies to legitimate sister websites and not 100 websites about how to lose weight eating apples.

Here is the video from Google Webmasters: