Some are declaratively integrated in APEX for example respond-js is part of the Blue Responsive theme, some others are not, for example twitter-bootstrap and another part is used in some sample or packaged apps, for example jquery-flot.
Having those libraries already there, means you can more easily integrate those in your own apps yourself too. Remember, if you want to go the extra mile it's worthwhile to create an APEX plugin so it's easier to reuse.
If you want to know more about those libraries, you find the links below:
|Library||(latest) version in APEX||Latest version of library|
|jquery||1.7.1||1.9.1 / 2.0.0 (no support IE6/7/8)|
|jquery-autocomplete||1.1||deprecated - part of jQuery UI|
|jquery-jstree||0.9.9a2||pre 1.0 fix 2|
So note that APEX is not always including the latest version of the library.