It makes up the majority of the mass of the Universe, yet it's invisible...so what is it?
Physics has often been considered a model for what a modern science should look like with its strong emphasis on observational or experimental verification of theoretical ideas. It's a discipline where hard facts are supposedly favoured over thought experiments relating to the unobservable. Yet physics also has a history of ideas about substances that are not only bordering on the unobservable but also have elusively outlandish properties. In the last decade for instance astronomers and physicists have come to the conclusion that about 95% of the matter and energy content of our Universe is so surreal that it is said to be "dark". So is this branch of science back to postulating the existence of things unseen?
Mankind has for a long time had the tendency to believe that at the bottom of all truths was something material, something mechanical. As a result the phenomenon of heat and heat transfer was for quite some time interpreted as the result of the flow of a "caloric fluid". But once Joule had identified the flow of energy, and Boltzmann had developed an interpretation in terms of the microscopic motion on molecules, the idea swiftly faded. Another similar idea was that of the "Aether". Maxwell’s laws for the electromagnetic field strongly resemble those for a continuous medium capable of displaying stress, shear and compression. The electric and magnetic fields were originally thought to describe the response of some ill-defined, unseen material called Aether, to stresses and strains. This material had to have odd properties because the Earth and the Planets were able to move through it without any resulting friction. However, the enormous speed of waves in the Aether, the speed of light, requires a rather extreme rigidity of the material. In a sense, Aether was extremely hard while being ridiculously sparse. It wasn’t until the end of the 19th century that measurements were conclusively showing that the Earth was not moving at all with respect to the Aether, thus further increasing the list of paradoxical properties. Einstein realized that Maxwell’s law does not need a material basis and that we should simply accept the electric and magnetic fields as physical quantities in their own rights.
The first signs that we were somehow missing out on part of the matter in the universe came from observations on how fast stars orbit the centres of their galaxies. Using Newton’s laws and the observed distribution of luminous matter one can compute the velocities with which a star at a certain distance from the galactic centre should rotate. These calculations however did not match the observations. The way out was to consider the presence of non-luminous or "dark" matter. Another option, however, is to doubt whether Newtonian laws still hold, and indeed using the more accurate laws of General Relativity seems to ease the pain .
Yet there was more dark matter to be found. Studying the motions of galaxies in the clusters in which they are grouped also reveals that here and there mass is present gravitationally but remains unobserved. Also the "seeding" of the large scale structure of the Universe that we now see in terms of the various clusters of galaxies should be expected to be driven, in part, by the dark matter flying around. All of these considerations did not allow us to pin down any particular candidate constituent of dark matter. There are no known elementary particles, which would fit the entire spectrum of dark matter occurrences. So more radical departures from Newtonian mechanics were proposed such as the "Mond programme"  of Modified Newtonian Dynamics. Although it is not clear how these ideas can be reconciled with general relativity, a relativistic version of them has been found by Bekenstein just a few years ago.
The pattern of dark matter wagging its tail also suffers from a certain degree of randomness, as some galaxies seem to consist almost exclusively of dark matter whereas others are practically devoid of it. So are we betting our scientific bottom dollar on yet another unseen material that needs to combine more and more contradictory properties?
Often the dark energy issue is thrown into the same bin as the dark matter question, although it is very different. For dark matter we don’t have any real theory. We don’t know what it is and we don’t know how it behaves. But around 1998 evidence started to accumulate that the expansion of the Universe was not slowing down, as was expected, but rather increasing. This is often worded as "evidence for the existence of a negative pressure" otherwise known as "dark energy". However, this is a bit of sales talk as the equations of General Relativity have no problem explaining such a phenomenon in terms of what GR calls the "cosmological constant".
When Einstein derived the equations of his theory of gravity he quickly realised that static universes were going to be difficult to get. He favoured those and in his search for a way out he discovered that his equations were not the most general ones, that another term could be added - the tantalising cosmological constant. It's a fact that nobody really knows where it comes from, but at the same time nobody knows why it shouldn’t be there. At the moment we have no reliable way of estimating or calculating the value of the cosmological constant on the basis of elementary particle physics. The only estimate known is off by about 100 orders of a magnitude, probably the worst prediction physics ever made. The reason for the appearance of the cosmological constant is usually sought in the dynamics of the matter content of the universe. However, Einstein’s theory would just as well allow us to see the cosmological constant as a geometric property of space-time rather than a property of the matter in it.
Prospects for a dark Future?
It is tempting to think Physics is "losing it". However the recent switch-on of the Large Hadron Collider (LHC) in Geneva marks the beginning of the search for the Higgs Boson, the particle believed to be responsible for giving matter its mass. The chances are good that, if an unknown new form of matter is lurking in the dark of the galaxies, the LHC will be capable of reproducing it in the lab. It might be, however, that in 2015, 100 years after Einstein’s publication of his great General theory of Relativity, we will have found out that our ideas about gravity or mechanics were in need of modification when accelerations become very small. The dark matter effects are in this ball park, but also weird and hitherto unexplained behaviour of the solar system probes Pioneer 11, and a number of others, result from "anomalous" accelerations of the same small magnitude. Although Darth Vader has taught us to never underestimate the power of the dark side, fresh light will probably be shed on the dark side of physics very soon.
 For a nice collection of sources on Mond see http://www.astro.umd.edu/~ssm/mond/
 The cosmological constant: http://relativity.livingreviews.org/Articles/lrr-2001-1/index.html