The formatting and styling is a little dated and claustrophobic, but I always liked how thoroughly (with plentiful links to convenient test examples and a dev console) the New York Times documented their APIs: http://developer.nytimes.com/docs/congress_api

Does language documentation count? If so, http://docs.racket-lang.org/ is probably as good as it gets.

I've always found Qt's docs very usable: http://qt-project.org/doc/qt-5.1/qtwidgets/qmainwindow.html

Also, although not an API, the diagrams in the SQLite docs are extremely helpful in structuring statements: http://www.sqlite.org/lang_createtable.html

I like the way the Stripe documentation is done. I've seen other tools/libs use a similar format but I'm not sure what the underlying doc generator is.

In PHP I generally use a framework called Yii. Their documentation is amazing: http://www.yiiframework.com/doc/api/1.1/CActiveDataProvider

I think Parse has really great documentation.

stripe docs