With the latest patch, you can set a waypoint which will appear as a white beacon on the main viewport. Go to your system map and click "View/Set Waypoint", then control-click where you want to set it. Your ship won't auto-navigate there or anything, and you can only have one waypoint at a time, but it's a start... maybe when the elusive third patch comes out we can convince Aaron to put in more/better waypoints
As for boarding, there is no boarding (again, we can only hope for it to be added, but Aaron is very attentive to fans of the SE games); you can only capture cargo by destroying the ship carrying it, letting someone else destroy the ship, or waiting for the ship to ram into an asteroid.
