The linked whygeo.com answer (Cai's) provides a pretty great high-level overview of the differences.
In more low-level terms, OpenLayers is an older library that is pretty heavy (http://openlayers.org/dev/OpenLa… is 854kb), but is pretty cross platform, while Polymaps is extremely light (http://polymaps.org/polymaps.min.js is 30kb).
OpenLayers also supports IE, while Polymaps, due to being reliant on SVG, does not (until IE9). OpenLayers supports OpenGIS formats while Polymaps leverages GeoJSON quite heavilty. Which is to say, OpenLayers is the older workhorse, and Polymaps is the younger, faster, meaner entry.