This is the checklist of specific code to review when upgrading prototype.js versions:

wonder_inplace.js
* overrides features of Ajax.InPlaceEditor

wonder.js
* Ajax.StoppedPeriodicalUpdater extends Ajax.Base
* Ajax.ActivePeriodicalUpdater extends Ajax.Base
* Form.Element.RadioButtonObserver extends Form.Element.EventObserver
* AjaxSubmitButton.observeField works around a prototype bug with observing radio buttons
* Prototype.exec brought forward

prototype.js
* Form.Element.Methods.serialize, element.getValue() was failing in a crazy case -- switched to Form.Element.Methods.getValue(element);

ibox.js:
* added _pub.init function to support reinitializing iBox
* added X-Requested-With header so iBox requests are recognized as Ajax requests

controls.js
* replaced Autocompleter.markPrevious, markNext, added line to getEntry (Wonder-406) 