Someone just tweeted at us earlier about GeoJSON (http://geojson.org/) which looks pretty awesome for storing polygon data. It sparked a conversation internally about a feature like that, especially since SimpleGeo (which offered that, I believe) is gone.
That point aside, geofencing queries are coming soon. That means that instead of just giving a center point and radius in your query, you can query with a polygon defined by arbitrary points and we will return your objects that exist inside that shape. Perhaps that could hold you over for the time being?