Yes. Use the suppressMarkers option on the Directions Renderer, then
add your own markers with click listeners that open an infowindow
("popup") with whatever content you want in it.
Here is an example that renders the directions result from scratch,
but it shows how to add markers at the start, waypoint and end.
http://www.geocodezip.com/v3_GoogleEx_directions-waypointsF.html
-- Larry