The neutrino, child of desperate remedies
Physicists might be tempted, at this point, to assume that placeholders are limited to the realm of a softer science like biology. The history of the neutrino, however, shows otherwise.
Like genes, the neutrino was proposed decades before it was first detected. And, unlike genes, it was proposed simply to make the numbers add up. In the early studies of nuclear decay, it was possible to track all the energy and matter—a photon, an electron, and the remaining nucleus, as well as the momentum of the matter—with decent precision. Unfortunately, all that energy didn't add up. This may sound trivial now, but the discrepancy was large enough that Nils Bohr seriously considered giving up on the whole idea of the conservation of energy.
A placeholder saved the day: the neutrino, a hypothetical particle that we couldn't detect but which carried away the missing energy during nuclear decays. It was nothing more than a hack to balance the books on things, and even Pauli, the man who proposed it, called it a "desperate remedy." But the physics community was apparently relieved, and a number of years later, Fermi's description of the weak force that tears atoms apart included a neutrino, largely settling matters.
But the neutrino remained a placeholder, in the sense that, even though all the equations called for it, it had never been detected. It took until the 1950s for physicists to pick up hints of its existence by blocking all the radiation coming from a nuclear reactor and seeing what still hit the detector. From there on out, physicists were assured that the massless neutrinos that were slotted into the Standard Model were a physical reality.
But that wasn't the last time that neutrinos and physical equations had an uneasy relationship. The physicists who modeled the Sun could, based on their understanding of fusion and the amount of energy coming from the Sun, estimate the number of neutrinos that would find their way to Earth. But, as we began to build more sophisticated detectors, we simply couldn't spot anywhere near that number. Physics was faced with a serious neutrino deficit.
The folks who worked on the Sun were pretty sure they had their numbers right, which meant that, once again, there was something about the neutrino that we didn't know about, but was essential to balancing the books. An alternate possibility existed: neutrinos underwent what are called flavor oscillations, so that an electron neutrino would, with some probability, oscillate into a different type, such as a muon neutrino, and thereby escape detection. But most people considered this ludicrous because of its implications. For oscillation to occur, neutrinos must actually have mass.
For all but a few specialists, this remained ludicrous right up until the day that Japan's Super Kamiokande detector confirmed that neutrinos did, in fact, undergo flavor oscillations. (It did this by comparing cosmic ray events that occurred directly over the detector to those that occurred on the opposite side of the planet, and sent neutrinos through the entire diameter of the Earth.)
The role of placeholders
Despite the radically different fields in which placeholders have been used, they share some basic similarities. In each case, we had a theory or principle that seemed to hold in lots of familiar cases. Traits are inherited; they show independent assortment; energy is conserved; fusion occurs the way we think it does. Putting a placeholder for something we didn't understand allowed scientists to work with very powerful theories, like evolution, genetics, and the weak force.
Placeholders either enabled or preserved some very scientifically useful theories. And that's precisely what we've seen with dark matter. Relativity, which we've measured to very high precisions, appears to apply throughout the Universe. But, on scales from galaxies through to the structure of the Universe itself, everything acts like there's more mass there than we can see. So, it's not especially outrageous or unprecedented to suggest that there's mass we can't see, and slot dark matter in as a placeholder in order to retain relativity.
All that's left is to actually find the particle, something we seem to be getting closer to. As we've studied more instances where dark matter shows its influence, we've actually eliminated a number of candidates, leaving us with a WIMP, a weakly interacting massive particle. Many people are expecting one of these to pop out of the LHC before too long, just as the neutrino finally was nailed down decades after we found the need for it.
So far, dark matter looks like a pretty good placeholder. Right now, however, nobody even has any idea what dark energy might represent, so there's not much of a place to hold, as it were. That's likely to change as more attention is given to this mystery, though.
When placeholders go bad (and why it's not so bad)
Those offended by placeholders will often reference some of the more famous ones that turned out to be dead ends, like phlogiston, luminous aether, and the epicycles used to maintain circular orbits long past their sell-by dates. These were also used in place of a natural phenomenon we didn't understand well, but ended up being thrown out and replaced. Maybe a placeholder like dark matter is a big mistake, and we'll be laughing at the gullibility of today's scientists in the not-too-distant future.
I'd argue that it really doesn't matter. Even when a scientific idea is wrong, as Kuhn suggested, it can still be useful if it helps organize a program of research.
Epicycles were discarded not because they didn't exist, but because a different model made better predictions about the orbits of the planets. Arguments over the existence of phlogiston helped spawn the birth of analytical chemistry. The concept of luminiferous aether made enough predictions that it was possible to demonstrate that it almost certainly didn't exist well before Einstein came along.
Based on the evidence and the confidence of cosmologists, I expect that we'll eventually discover the particles that produce the effects we call dark matter. But, even if we don't, I also expect that the search for these particles will have led us to some very interesting physics, and whatever replaces dark matter will be more interesting still.