I was playing a mission (I think it was a mission from an old campaign called "unification prequel" or something), and after it ended there was an allied Hatshepsut destroyer in the area, and just for kicks I decided to fly into its fighterbay. I was expecting to hit a wall a little ways in but to my surprise I found myself flying through a tunnel leading to a room which was a mockup of the Vasudan main hall screen from the original FS2 campaign. There was also a reactor subsystem which was targetable inside that chamber (those wacky Vasudans, putting their ship's reactor right next to an important command area). There was also a tunnel on the other side leading out.
Anyway, I thought that was neat, and now I'm wondering if the modding team has left any other neat little surprises like that around.