Twitter's Bootstrap 3 will be released soon. Twitter Bootstrap bundles some Javascript plugins. All except the Typeahead plugin are migrate to Twitter Bootstrap 3. Many other plugin are written for Twitter Bootstrap 2.x how to migrate them to Twitter Bootstrap 3?
Related question:
Download the plugin's source code Javascript and CSS (or less) and replace old class references with new, see: http://www.bootply.com/bootstrap-3-migration-guide.
Beside the class names changes most Javascript code should work.
Do the same for your HTML code. Or use a migrator/updater like: http://twitterbootstrapmigrator.w3masters.nl/, http://bootstrap3.kissr.com/, http://code.divshot.com/bootstrap3_upgrader/ or http://upgrade-bootstrap.bootply.com/
When your plugin use Glyphicons: Install Glyphicons from http://glyphicons.getbootstrap.com/: download the files and copy over all the font files to a /fonts directory near your CSS. Include the compiled CSS file from the /css in the repository to your local css folder or download the Less file and compile it with your Bootstrap files. Twitter Bootstrap 3 includes 200 glyphs in font format from the Glyphicon Halflings set. To include them class names change from icon-* to glyphicon .glyphicon-*.
When your plugin depends on the Typeahead plugin you will have to rewrite your Javascript to adopt: https://github.com/twitter/typeahead.js/ or find a other solution. Bootstrap dropped its own typeahead plugin in version 3. They advice to use Twitter Typeahead. Twitter Typeahead needs some fixes to work with Twitter's Bootstrap 3, see: https://stackoverflow.com/a/18171568/1596547. For simple autocomplete use cases there seems nothing wrong with the dropped typeahead plugin. For this reason you could also decide to keep the "old" plugin: https://github.com/bassjobsen/Bootstrap-3-Typeahead. See also: https://stackoverflow.com/questions/18615964/ajax-call-in-bootstrap-3-0-typeahead/18620473#18620473
Twitter Bootstrap 3RC1 seems to use jQuery v1.9.1. See also: Does Twitter Bootstrap include jQuery?. Include plugins should work with the latest version of jQuery. So test your plugin with the latest version too. NOTE the new 2.x version of jQuery drops support for IE8 so this version is not compatible with Twitter Bootstrap 3 which should support IE8.