I use Jux2 as a meta engine but also as an easy way to check search engine overlap between Google, Yahoo, and Ask Jeeves. Chris explains search engine overlap in this 2004 article about another cool tool called Ranking.Thumbshots.com. More info about search engine overlap on this page.
Tabs on results pages now allow you to move easily between four types of results:
+ Best Results (Results merged into a single list from all three engines)
+ What "Google is Missing" (Results in Ask Jeeves and Yahoo but not Google)
+ Results that Only Google Found
+ Direct link to Google results page
Also, on the right side of the page you'll see a Venn diagram that illustrates each type of search. Jux2 used to offer some summary numbers here about the amount of overlap found in each query. I hope they bring them back.
We've also learned that Jux2 will soon add MSN Search to their service. Good news!