All you have to do is choose the option to "dynamically extract links from this page and add them to my search engine" for your site. You have three options: include only the individual pages linked from your site, include the subdomains or the entire sites, even if you only link to a page.
If you don't have this feature you can test it at this page or in this blog's search box.
A search for "Safari" returns the homepage of Apple's browser and a site that offers a way to preview a site in Safari before my post about Safari and that's a fair enough. That post linked to both sites that are ranked higher.
The feature has already been available in Lijit, a site that let you "easily create your own search engine, which searches your blog, blogroll, bookmarks, photos, and more", but now it's a simple option in Google Co-op. Here are the results for "Safari" in a custom search engine built using Lijit.
You can use this for feeds, directories or for sites that collect a lot of interesting links. Bloggers could dig deeper in their archives and rediscover useful links, while readers have more comprehensive search results.
An important drawback is that if you enter the homepage of a site, Google will retrieve the links only from that page, even if it will continue to monitor it for new links. Also the search seems to be somewhat slower and the results may appear diluted.
But, as the Custom Search blog says, lazy people can rejoice. "If you have a blog or a directory-like site and don't feel like listing all of the URLs you want to search across, you can leave the work to us. With this new feature we'll automatically generate and update your CSE for you."