Other than the TOS black star, the naked singularity of the Romulan engines, and the Enterprise episode "Singularity", were there other references to black holes in any of the Star Trek TV shows?
Interestingly, the term "black hole" seems to be mostly abandoned by the 23rd century, according to Commander Deckard in Star Trek: The Motion Picture
DECKARD: Captain, Voyager 6 disappeared into what they used to call a black hole.
This perhaps explains why the term "black hole" is encountered so infrequently throughout TOS, TNG, DS9, and Voyager, despite frequent references to seemingly similar phenomena. However, there have been a few nominal references to black holes throughout the later TV series:
In TNG "Deja Q", Q hypothesizes that a moon's orbit was destabilized by a black hole. No such object is ever seen, however.
In TNG "Timescape" Data concludes that a species of alien uses black holes are "nests." Again, they only mentioned, not seen.
In VOY "Hunters", Kim and Paris refer to a quantum singularity being used as a space station's power source as a black hole:
KIM: Commander, if my sensors are right, that station is using a quantum singularity as a power source.
PARIS: A black hole?
KIM: It's a tiny one, probably about a centimetre in diameter, but it's putting out almost four terawatts of energy.
Additional references to the object as a "black hole" later in the episode confirm that Paris's nomenclature is at least informally correct. Furthermore, this marks the only time in the series where we see a black hole "in action" when the singularity's containment fails and it destroys the station and two Hirogen vessels.
Now that we have established that "quantum singularity" is a synonym for "black hole", we can also include the object from VOY "Parallax", which possessed an event horizon and trapped Voyager inside it. As Voyager was unable to leave the event horizon even at warp velocities, this probably meets your criterion of having an escape velocity greater than c.
The series are replete with references to other varieties of singularity, but none resemble black holes as we understand the term.
In The Motion Picture, Voyager 6 is said to have disappeared into "what they used to call a black hole", although given that it was spat out elsewhere in the galaxy it seems more like a wormhole (at least as the term is used in other Trek media).
"Singularity" is also used to refer to the aperture of a wormhole or similar "tunnel" on several other occasions in DS9 and Voyager.
In The Next Generation 3x13 "Deja Q" (the one where Q is turned human), there's a passing reference to a black hole having caused the disaster of the week when it passed through the system, destabilizing the orbit of an inhabited planet's moon.
Also in The Next Generation are the Romulan ship engines, which run on contained singularities as you mentioned. The Hirogen also used this technology at least once, in Voyager 4x15 "Hunters"; Voyager disrupted the containment field around the singularity, causing it to explode into a black hole.
Voyager also encountered a kind-of-but-not-really black hole-like "singularity" in 1x03 "Parallax" which they were trapped in for awhile.
As you mentioned, in Enterprise 2x09 "Singularity" the Enterprise encounters a trinary system where one of the stars is a black hole, and runs into problems while trying to survey it.
In Star Trek, the JJ Abrams reboot, black holes generated from "red matter" are used as a doomsday weapon.
In Discovery 2x08 "If Memory Serves" there's a fake black hole, used as a deterrent to entering the Talos system.
Aside from a handful of uses as a generic space hazard ("Singularity", "Parallax") or as a volatile power source ("Hunters", several uses by the Romulans, the reboot movie) black holes don't seem to have made much impression on the franchise, perhaps because by definition they don't really do anything aside from mindlessly threaten our protagonists.