jQuery and MooTools both are feature-rich javascript libraries used by developers to traverse and manipulate HTML documents in a simpler and more convenient way than the Document Object Model or DOM (which is the original API supported by all browsers) can provide.
Until Joomla! 3, MooTools was the scripting language of choice and was packaged with the framework. Frontend functionality such as modal popups, caption... was handled by MooTools. The jQuery library was loaded mainly by extensions and templates which started to use this newly popular library.
Since Joomla! 3, MooTools is phasing out update after update and is being replaced with jQuery (which is now the official library packaged with the Joomla! framework). Although MooTools is disappearing from Joomla, templates and extensions may still use it, therefore loading their own version of the library.
Library conflicts will most likely happen for some time...
