Interesting question. I found about 20 systems that I could identify as real stars. Gx,Gy and Gz are their galactic coordinates while x and y are their position on the wing commander map.
Here they are:
name,Gx,Gy,Gz,x,y
Capella,-40.2,12.3,3.77,120,1485
Castor,-47,-6.44,20.2,120,1591.667
Pollux,-16.74,4.305,-25.72,114,1455.667
Barnard's Star,4.936,3.001,1.388,138,1453.667
Procyon,-9.179,-6.22,2.674,120,1675
Alpha Centauri,3.165,-3.048,-0.0818,120,1920
Arcturus,12.98,3.517,34.16,144,2004
Proxima Centauri,3.165,-3.048,-0.0818,138,1980
Ross 248,-3.382,9.291,-3.008,120,1814.667
Sirius,-5.745,-6.275,-1.262,122,2080
Sol,0,0,0,127,1826.667
Proxima,3.165,-3.048,-0.0818,133,2456
Alcor,-14.5,35.7,71.4,136,3051
61 Cygni,1.438,11.27,-1.188,136,1303.333
Alpha Tauri,-61.3,-1.44,-21.9,134,1390
Polaris,-212,322,194,130,1684.667
Wolf 359,-1.896,-3.902,6.478,138,1544.333
Deneb,150,1592,52,74,2739.333
Antares,579,-78,151,94,2619
Tau Ceti,-3.49,0.373,-11.37,116,2746.333
Rigel,-580,-328,-306,117,2173
Altair,-28.85,-10.19,-2.345,94,1467
I plotted their positions in order to try to find some pattern. I suspect that the real positions of the systems were not considered when they decided to name the systems in the game. However, some patterns may still be found.
Edit: I removed the plot of the map data something was wrong with it.