Prototype and script.aculo.us stuff:

  prototype.js
  controls.js
  dragdrop.js
  effects.js

Google maps stuff: (I think this relies on Prototype.)

  gmaps.js            Google Maps API.
  clusterer.js        Add-on for Google Maps API.
  ym4r-gm.js          \
  geoRssOverlay.js     \ This is all part of YM4R.
  markerGroup.js       /
  wms-gs.js           /

Local scripts and extensions:

  cached_auto_complete.js   Replacement for Prototype's Autocompleter.
  donate.js                 Used by support/donate.rhtml; uses Prototype.
  edit_loc.js               Used by location/_form_location.rhtml; barely uses Prototype.
  element_extensions.js     Adds some useful methods to Prototype's Element class.
  image_vote.js             Used to enable ajax image voting wherever images appear; uses Prototype's Ajax class.
  name_list.js              Used by species_list/name_lister.rhtml: uses Prototype heavily.
  name_list_data.js         (auto-generated data for name_list.js)
  pivotal.js                Used by pivotal/index.rhtml; uses Prototype heavily.
  vote_popup.js             Used by observer/_show_namings; uses Prototype.

(last updated 20111114 by Jason)