What is the difference between archetypes and ontologies?

An easy way to think about archetypes and ontologies is based on undertanding what they say. Archetypes model information, while ontologies model reality. For example an archetype for "systemic arterial blood pressure measurement" is a model of what information should be captured for this kind of measurement - usually systolic and diastolic pressure, plus (optionally) patient state (position, exersion level) and instrument or other protocol information. In contrast, an ontology would describe in more or less detail what blood pressure is. This archetype tutorial (PPT) provides a detailed example on slide 12.

If in your philosophical view of the world, "information" is part of "reality" (and this is the strictly correct way to understand the world), then archetypes themselves constitute an ontology, whose subject matter happens to be information. Other "ontologies", as one tends to use the word today, have as their subject matter "reality" (other than information).

See the openEHR Wiki ontology page for more on ontologies and openEHR.