- You can customize the appearance of custom search engine using an XML API, which gives you more flexibility.
- You can turn off the ads.
- You get dedicated phone and email support.
- And you can remove the Google logo from the search results.
Chris Sherman details the pricing, which I cannot find on the Google site.
Google Custom Search Business Edition is available for $100 per year for sites up to 5,000 pages, $500 per year for up to 15,000 pages, and $15,000 or more for sites with a million or more pages. For smaller sites, businesses can sign up using a credit card for payment, and get a site search up and running quickly using a simple online interface.
Forum discussion at WebmasterWorld.