There’s certainly theme potential in Spock/Data/Odo/EMH/Seven/T’Pol discovering their fundamental humanity, but it was more often a plot device beaten to death than a theme developed over the course of a series. The Borg were also overdone, making them both less of an intentional theme than a weekly writing cop-out.

Or I’m just pessimistic that way.

Admittedly, I haven’t seen every single episode of these shows (that’s why I bought a full set of TNG and am watching them now), but I seem to recall that these issues did keep recurring. Which, to me, reads as intentional.

A cool sci-fi concept is not in and of itself a theme - so Q’s trial of humanity was more of an idea tossed out there for the fans to expand in their own minds (a typical approach in sci-fi) than the sort of underlying thread of feeling that makes a literary theme. I can’t think of anything in TNG that compares to, say, Spike draped over a cross for foreshadowing (see MustangSally) or the Glory arc for continuity. DS9 may have had themes, but I agree with Liz that the rest of Trek has them unintentionally, if at all.

Look at Voyager, a show which set itself up as having very limited arcs. Despite the fact that I know TPTB disliked most elaborate forms of continuity, themes or arc-concepts, I still see season 5 as Janeway’s descent. It started with her depression in “Night”. Contrary to canon, I don’t see her as having fully recovered from that until the catharsis of “Equinox 2″. The fact that said catharsis involved basically torturing a Starfleet officer only makes Janeway’s darkness more interesting to me.

(Interesting enough that I basically gave up on the show shortly after she returned to her perky norm.)

That’s a theme, but I don’t believe it was there by plan or intention.