I think that the type of software you are looking for is called a chart plotter software. There are several solutions used in navigation, where using a laptop is more and more common. I will not list here the solutions using dedicated hardware (AIS/navigation systems for example).
Amongst paying options you have the "best seller" called MaxSea (http://www.maxsea.com/products/software) that includes 3D navigation, waypoints, tides, weather etc... Their competitors include Expedition Marine (http://www.expeditionmarine.com/) used by Volvo race. They basic do the same thing, with small variations of course.
However, you were looking for free solutions. I can list two that I have used sailing, with a preference for the second one.
The first is called SeaClear (http://www.sping.com/seaclear/), which is a Windows based chart plotter. It can connect to a GPS, and be used as a route planner. Raster nautical charts are supported and you can calculate some additional features (time, fuel consumption) according to data you input (wind, currents, tides). Personally, I don't really enjoy the interface, and had some problems with the software freezing and not recognizing my GPS device.
The second solution I proposed in my comment, is Open CPN (http://opencpn.org). It has seen many developments over the last few years, offering a more intuitive interface and more options than SeaClear. You will find a complete list of functionalities on the website, plus there is an active developing community that back the project up. For me the most useful functionalities are the Tide and Current prediction, Route planning with tidal support and autopilot output.