I know
Deep Space Nine has had the rep as "The Dark Trek Show" since what seems like the day it was announced, but overall I don't think it's justified. It definitely questions a lot of the underlying nature of Roddenberry's vision for
Trek, and used the pressures of the Dominion War to play with those ideas to show how the characters and Federation either can or can't hold to those ideas of a humanity that's "evolved" past social faults.
However, in the end, I think the fact DS9 goes there but still shows how the characters and others still believe in the "root beer" validates those ideas instead of engendering cynicism about them. Even with the Federation, the ideals bend and break at points but at the end of the series I never get the feeling they’ve crossed a line from which they’ve accepted those hard choices as the new normal. In that way, I always take DS9 as reaffirming Roddenberry’s values. When Ross and Sisko refuse to share Martok’s bloodwine over the dead Cardassian bodies at the end of the Dominion War, there is a human decency which I think gets to what Roddenberry wanted.
ODO: Am I the only one who's worried that there are still changelings here on Earth?
JOSEPH: Worried? I'm scared to death. But I'll be damned if I'm going to let them change the way I live my life.
SISKO: If the changelings want to destroy what we've built here, they're going to have to do it themselves. We will not do it for them.
Also, I think there's an argument to be made that
Strange New Worlds, even with the Klingon boy bands, is a "darker" show than
Deep Space Nine.