Successfully complete the game with the indicated race to unlock the corresponding bonus:
The Breen: Sha Ka Ree map for Skirmish mode. This is the "God" system from Star Trek V.
The Cardassians: Borg Unicomplex map for Skirmish mode
The Dominion: Xindi Skrimish Set, which includes the Reptilian cruisers and Insectoid fighters
The Federation: Second Federation Skirmish Set, which includes the Sovereign, Nebula, and Oberth vessels
The Klingons: Borg Skirmish Set
The Romulans: Talos IV map for Skirmish mode. This is from "The Cage/Menagerie" episodes of the original series.