Google started allowing people to roll-out their own search engines. This is a very powerful feature if you think about it. For example, university departments can have custom search engine that only brings results from a set of websites related to the topic of that department.
So, the key is to identify a group of websites that can be logically grouped to provide a more targeted search results. While that is the idea, given that Google’s cse (cse blog) allows up to 5000 links, people may come up with innovative use for such large numbers. For example, the search engine Publicly Traded Companies Search Engine provides search among thousands of publicly traded companies.
One good thing with Google’s CSE is that it allows for collaboration. So the 5000 links limit can be overcome, by working with other people to add more links. Ofcourse, as long as the set of links have that extra meta-data with them, this should be fine. But, abusing this to add any random set of links will not serve the intent. Good luck rolling out your own CSE.