We're doing some research in this area ourselves. Not a lot out there in terms of "gold standard" for website API references.
The most common website APIs referenced are:
- Google APIs http://developers.google.com/api-client-library/java/apis
- Amazon S3 http://docs.amazonwebservices.com/AmazonS3/latest/API/
- Twitter https://dev.twitter.com/
- Facebook http://developers.facebook.com/
- LinkedIn http://developer.linkedin.com/index.jspa
- Delicious http://delicious.com/help/api
- YouTube http://www.youtube.com/dev
- Netflix http://developer.netflix.com/
- Sun Cloud API http://kenai.com/projects/suncloudapis/pages/Home
Another list here:
http://www.pingable.org/the-top-15-web-apis-for-your-site/
Someone recommended the book Restful Web Services as a good reference on this.
(please feel free to edit the above list to add other high profile websites with APIs)
