I prefer to set: fullresolution=0x0 (desktop native) output=overlay And for sound I increase the block size to around 2000. I've always found this gives better performance in fullscreen and will stop any weird sound skips and pauses with nice crisp pixels.
Many users are reporting issues with the sound in GOG's release of Wing Commander I. Specifically, they are hearing sounds like chime notes intead of lasers blasts during combat. The problem is that the game is configured to play sounds through a Roland MT-32 MIDI, which DOSBox does not naturally emulate. We expect GOG will provide an updated version of the game in the near future, but in the meantime this quick user fix will repair the issue: open the WINGCMDR.CFG file in a text editor and replace the letter "R" with "a552".