There are three versions of the game you can play:
Sins of a Solar Empire (vanilla)
Each version includes all of the content from the previous version(s), meaning you can't play Diplomacy without Entrenchment's starbases (but why would you want to? Starbases are the coolest!).
Trinity is the name of the compilation of all three. It's like saying "Sins of a Solar Empire: Complete", only way cooler. Trinity is completely compatible with the non-Trinity copies of the game, so you can play multiplayer with someone that only has vanilla, and they don't have to worry about buying more just to play with you. You'll simply need to select the vanilla version in order to play with them.