Zope 3 evolved out of Zope 2, and was originally intended to replace the latter. Today, Zope 3 refers to the new techniques and APIs such as the component architecture, that have migrated back into the Zope 2 project as well as other projects such as pyramid, Grok and BlueBream.
Zope 3 evolved from Zope 2 and improved the development experience through the use of a component architecture.
It was originally intended to replace Zope 2; today (2011) it is packaged as the Zope Toolkit libraries, which are the basis for the Grok and BlueBream web frameworks and also for the ever-evolving Zope 2, now known as "Zope" again. You'll also find the same component architecture and techniques in pyramid.