Yesterday's Mashup of the Day was a fun one for those who miss the good old days of command shells, goosh.org, "the unofficial google shell". Developer Stefan Grothkopp coded this on top of the Google Ajax Search API to give you a command shell for interacting with Google search queries.
Microsoft is one of the first--and certainly the largest of--customers of Wolfram Alpha's commercial API (our Wolfram|Alpha API profile). For math and nutritional searches, Microsoft's Bing now uses Wolfram results.
It's always exciting to see those outside the web industry using an API to improve their sites. NY Times First Look blog has a great example of what Dallas Public Library has done with the Best Sellers API.