I can't say much for TOS as I've only seen a few episodes but having watched TNG and DS9 several times I can think of a few episodes worthy of intelligent sci-fi:
TNG: A Measure of a Man, Q Who, Who Watches the Watchers, Sins of the Father, Yesterday's Enterprise, Sarek, Family, Brothers, The Drumhead, Darmok, I Borg, The Inner Light, Chain of Command, Tapestry.
DS9: Emissary, Duet, In the Hands of the Prophets, Necessary Evil, The Wire, Improbable Cause, The Visitor, Rejoined, The Quickening, Broken Link, Children of Time, Far Beyond the Stars, In the Pale Moonlight, Inter Arma Enim Silent Leges.
Those were episodes that left a strong impression on me and they still do, I'm probably missing a few dozen others. Ultimately I think ST main strengths were its morality tales and characters with moral integrity- for the most part. In terms of psychoanalysis or character exploration, I think DS9 has an edge over TNG.
Was it all scientifically plausible? No, not by a long shot. But since fans are still talking about the Borg, the Founders and the Prophets then I guess these were races worthy of intelligent sci-fi.
Intelligent sci-fi seems to be anything that is thought-provoking and is so iconic that people still talk about many years later. Consider 2001, The Matrix, Solaris, Alien and other science fiction films that are still talked about today. All intelligent sci-fi IMO.
Lastly I think we fans are thinking too hard about Star Trek and we're nitpicking it down to its bare bones, and when you do that for a long time I think you lose sight of the magic of Star Trek. But if we didn't nitpick then these forums would be very empty...