For Star Trek, in-universe this happened at least twice. The relevant episodes are TOS 2x22 Return to Tomorrow [0] and TNG 6x20 The Chase [1].
VOY 3x23 Distant Origin [2] also in-universe establishes convergent evolution is very likely to create humanoids (makes no reference to the other two episodes, as far as I remember, but it's kinda wishy-washy in that it could be highly likely because of the two progenitor species).
That said, there's plenty of non-humanoid aliens. Off the top of my head: Q, the Tholians, the Caretaker's species, the two aliens from TOS 2x01 Catspaw (shown to be tiny and kinda birdlike in the final scenes), and Species 8472.
Oh, I was referring to progenitor seeding specifically. In terms of interbreeding, there's a few more prominent ones: Spock, B'Elanna Torres, and Alexander Rozhenko and B'Elanna's daughter (who are respectively 3/4 human and 1/4 human, showing there likely isn't an infertility problem like with mules [0]).
(Though I admit that the ENT example was certainly unique in the differing biologies)
Dangit I changed the order of "Alexander Rozhenko" and "B'Elanna's daughter" to make it clear they're not related, and forgot to switch the 3/4 and 1/4. Alexander is 1/4 human.
Of the two relevant episodes in my other comment ( https://news.ycombinator.com/item?id=24726335 ), the TOS one explicitly states that that seeding doesn't apply to Earth because of the fossil record and when it occurred (but could explain some of Vulcan's history), while the other one was so early on that Earth was still in the primordial-soup stage.