I can't find a lot of information detailing the main differences between these two source ports. Both claim to be 'purist' while adding fixes and improvements, and both look like they use much of the same resources. The only couple of things I can see that really stand out is that Parallel Universe chose Tortoise SVN as a distribution platform, and Gemini Gold has more up-to-date news on their main page (by about one year). They both look like they have about the same amount of 'additional content' (mods and plugins and the like), and neither one looks like it has better graphics than the other.

Gemini Gold looks a lot less unpolished than Parallel Universe does, in the sense that there are less "Placeholder" names for missions, equipment, people and places (example: "weapon_bolt_heavy_fusion" should just read "Fusion Gun" in the menus). I suppose that's what happens when a project loses focus.