A second-class citizen was an individual who belonged to a social or political group which had been systematically discriminated or prejudiced against, despite being a citizen.
In 2155, Josiah believed that Human beings would become second-class citizens on their own world as a result of increased alien presence, particularly that of Vulcans. (ENT: "Demons")
In 2375, Worf noted that the Cardassians were a proud people but the Dominion treated them like second-class citizens. (DS9: "The Changing Face of Evil")
In approximately 3074, The Doctor's EMH backup module cited being deactivated while speaking mid-sentence as an example of being treated like a second-class hologram. (VOY: "Living Witness")