The various and independent inclusion of scripts by plugins and templates is one of the tricky points in TYPO3. As far as I know, this point cannot be managed at one single point.
There is a plugin "t3jquery" that offers to build, compress and share a common jQuery library. It also has a service to analyze other plugins for their dependencies. But this doesn't solve the problem in general, as many plugins don't check for libraries already loaded.
The most stable way is to remove all plugin's references to libraries manually in your TypoSkript. This gives you some simple additional TypoSkript lines. I use lines like these:
plugin.tx_imagecycle_pi1.file.jQueryLibrary >
plugin.tx_imagecycle_pi1.jQueryLibrary >
plugin.tx_multicontent_pi1.file.jQueryLibrary >
plugin.tx_multicontent_pi1.jQueryLibrary >
# Fluid
page.headerData.998 >
You can find the matching TypoSkript descriptors by searching for the library name in the TypoSkript browser or by greping in the plugin's source code. You will also need this if you wish to add libraries as part of content that was get by AJAX, thus separating the libs from the page content.
Here's a tut (in German): http://jweiland.net/typo3/typoscript/javascript-manuell-entfernen-oder-einbinden.html
Futher possibilities you can check:
- Some plugins are written in good structure and offer to keep back their Javascript in the settings.
- Some script inclusions may come rather from the static template but from a plugin, so don't forget to have a look there.