Firstly, am I correct that the image shows a polygon to point relationship? If so you want to make sure that the polygons stand out more and should visually match the links. I would suggest choosing a group color (say blue), use light blue polygon fill, a dark blue border (helps the eye resolve the edge of the polygon) and medium blue for the link (associates the link with the polygon).
I would not use color to express the flow volumes in the links as you have done above, it will probably be too busy with lots of links, width and transparency are the variables to play with.
Secondly, the essence of the problem is volume of data, it isn't possible to produce a simple graph of the suggested 1000+ network as the visualization would be very cluttered. The two main suggestions so far seem to be to collate edges together (tree visualization) or to produce a graph where disconnecting the locations from real space in effect creates more space to visualize the connections (in the same way by losing true locations the famous tube map of London creates more 'space' in the centre of London to help visualize the connections between tube stations that are very close together). Both these have value but the graph has the obvious disadvantage that you whilst you've visualized the network, you have lost the real spatial positions.
An alternative is to cope with the data overload by splitting the data into groups. If there are no logical groups then directional segments (N, NE, E etc) is a possible way to do it. I would build a visualisation where all the relationships are grayed out, on mouse rollover the relevant polygons and links appear in bold color. A sub option would be to work the mouseover via toggle clicking or radio layer buttons where multiple sections could be chosen at once.
You could also produce an animation where the links are shown as 3D loops and the segments are ungrayed one by one with the camera viewpoint changing to make maximum use of the 3D (see http://senseable.mit.edu/obama/the_world.html which shows what I mean by loops and camera view changes). After the animation is shown, users could be allowed to explore the map freely with radio buttons controlling the segments or groups of data.
This is not that complex to achieve using Google Earth client or API and kml, I've blogged about producing loops here http://googleearthdesign.blogspot.com/2009/09/loop-links-in-google-earth.html and tours here http://googleearthdesign.blogspot.com/2009/08/creating-tours-howto-2-turning-elements.html. kml is pretty easy to work out http://code.google.com/apis/kml/documentation/.
Whilst I'm always one to worry that 'flashy' visualisations are clever but ineffective, I suspect this one will work be effective and the bonus is that the 3D animation will impress most clients.