As a search engine, Google is one of the most popular place on the web where people search for something. There is a good reason for that, and that's because obviously Google knows a lot more than most.
Webmasters and web owners have long tried to appeal to Google and follow its guidelines in order to get their websites rank better. To determine a site's rank, Google looks deep into many factors, including finding more about the administrator of the site. By knowing who owns a website and who is the administrator, Google can use the information to take some actions it thinks necessary.
Knowing how Google knows what websites you control can give you more insight on how Google works. Furthermore, you can put some to your advantage, and at the same time create a work around to some of your problems.
When talking about a relationship between websites, search engines sees this as administrative relationship. As an administrator, you have control of the site, the contents, the links, subdomains, and many more. And because of that, Google thinks that it's necessary for it to know who is really working behind the scene of each website it indexes.
As Google tried to distinguish who owns what websites, Google is continuing its efforts to known the administrative relationship between websites. This can help many administrators. But at times, it can also be a disadvantage.
Related: The Reasons Why Your Backlinks Aren't Helping Your Search Engine Rank
The Advantages and Disadvantages
Google is one of the internet companies that have the most complete database of links that scattered throughout the web. By owning more than one site, Google can distribute the authority between your sites. Google can also reward websites for links that are related to each other, and this is an advantage for you if you can establish a relationship between the sites that you own.
You may want to tell Google that you own more than a site.
On the other hand, owning several websites can give you disadvantages. One of which is a link discount.
Google can give a significant link discount if there it found out that you own two or websites, and they interlinks each other. Google can also give other negative consequences accordingly.
The very good reason for this is because if you control how the links flow between two or more websites, for example, establishing relationship between those sites of yours shouldn't cost much. And the same goes to the opposite. If links are coming from websites you have no control, they should worth a lot more than links that you can control.
In short, links between sites that are controlled by the same entity shouldn't worth as much as links that are controlled by other people. This is why Google likes links to be created naturally.
As Google also index subdomains, the advantages and disadvantages also apply. And the same goes with multilingual websites.
A Stalker for a Reason
Google is also following people on the web. As it figures out the administrative relationship, webmasters and web owners can find themselves penalized and their links discounted despite they start a new website with a new domain.
To find our more about administrative relationships, Google has been looking at things like ownership, WhoIs records, the website's hosting company, IP address, CSS, custom JavaScript, AdSense/Analytics codes, Internet Protocol version and others.
Beside those, Google is also looking into link patterns and the website's contents. Google also take images as consideration. For example, if two of the same images are hosted on different sites with the same content, this could be an indication to Google that the sites are owned by the same entity.
And again, as Google has a complete catalog of links and contents on the web, using its analysis, it can determine what site is associated to whom.
Conclusion
With Google continuously scanning any changes webmasters and web owners do to their websites, in general, it's difficult to hide administrative relationship from Google. With the data it owns, as well as other data that are freely available on the internet, escaping Google is really not worth the effort.
Understanding Google works can give you clues as to why you're ranking high/low on the sites you own.
Further reading: How Search Engines Process Your Queries Determines Your Satisfaction