The Google Custom Search blog has announced the availability of Search Results Overlay for Custom Search Engine(CSE). Using AJAX techniques, you can now get your search results in an overlay that appears on top of the page containing the search box. Here's an example.
To integrate, go to the Code tab of your search engine's control panel and select "Host results on a non-Google site" and "overlay" to get this new code.
This new code is powered by the AJAX Search API, which gives you complete control of your search results and is easy to use with Custom Search.