I had written some applications in the past to calculate all possible links between stars.
I did a piece of work for Ad Astra games which used the data to calculate when each star system was open for colonization. In that game (Attack Vector: Tactical), it took about three years for an intrepid survey starship to refine the position of each jump entry point so that it could be safely used. I wrote an app that sent virtual survey ships starting at Sol to all direct neighbor stars, then gradually walked the entire map while keeping track of the years.
This set up the founding date for all the interstellar colonies.
I want to export such data to a 3D app such as Blender (which I use because it is free), and I will as soon as I can figure out how to automatically make the star labels perpendicular to the camera's view, regardless of how the camera moves.
The main thing that bothers me about the original Traveller 2300 map was the lack of either links or cartesian coordinates. They made the map basically worthless. Coordinates allow one to calculate the distance between stars. Links show you the distance between stars. Without either the map is a useless pattern of dots.
If you have fewer stars than the 23K map, you can get away with doing something like this map I made:
http://www.adastragames.com/graphics/Maps/DiagramMap%20J.zip
Another problem is indicating spectral class. More to the point, almost half of the stars are binaries or multiples. I generally just use the spectral class of the star with the brightest luminosity. There was a recent book of Star Trek maps where they had each system indicated by a dot color coded by brightest spectral class, with color coded arcs surrounding the dot for additional stars in the system.
I was also toying with the idea of using different symbols. A dot for an uncolonized star, a square for a homeworld, a triangle for a colony, a five pointed star for an outpost. This becomes a problem with the stars occupied by more than one nation.
I also wanted to color code the various "arms". Blue for American arm, etc.
If you wanted something off-beat, you can try making a map that requires red-blue stereo glasses to see it in real 3D.
As previously pointed out, with the stutterwarp system, the 3D location of the stars is superfluous information as far as the players are concerned. A "subway map" will do, like this one:
http://www.adastragames.com/graphics/Maps/TubeMap.pdf
http://www.projectrho.com/smap12.html
Galactic maps are pretty, but useless from a game standpoint:
http://www.projectrho.com/portfolio/port21.html