Various FS universe connections, not necessarily as clear-cut as the holed Orion model. Some are obvious, like All Your Base Are Belong to Us. Some rely on external information, like the Silent Threat secret video and the Cardinal Spear final mission.
Here is an incomplete list:
Phasing jump nodes
The Deneb asteroid belt
References to Echo Gate and Shrouding the Light
We didn't really refer to it, but we figured the Talus Particle Accelerator is the same installation that created the Helios
The GTF Angel and the Serkr
I was going to make an exhaustive list, but it's quite long and I don't want to spoil all the discoveries just yet. :p I suggest re-playing the campaign and looking for references to the FS universe, to other popular campaigns, and to famous legends or stories. A good place to focus your attention would be the various ship names, but there are other clues too. ;) There are also several fill-in-the-blank moments, where the player will not necessarily understand the significance of events on the first play through.
EDIT: And there's a whole other layer of secrets that only 56 people figured out, but that's a subject for another thread. ;)
We didn't really refer to it, but we figured the Talus Particle Accelerator is the same installation that created the Helios
Oh yeah, I remember that. I was like "Someone has far too much spare time". Very nice touch. :P