Scientists tend to believe that the elementary structures underlying the world we observe are ultimately simple and beautiful, even (or especially) the structures we have not yet discovered. Still, this basic elegance does not always manifest itself directly -- the universe we see is something of a mess.
This pie chart is a rather prosaic representation of a truly impressive accomplishment: an inventory of the relative amounts of the different substances comprising our universe. Yellow is ordinary matter -- atoms, molecules, dust, stars, planets, both visible and invisible -- or what cosmologists call "baryons" (since most of the mass of ordinary matter comes from the protons and neutrons inside atomic nuclei, and protons and neutrons are classified by particle physicists as baryons). Baryons make up about five percent of the known universe (actually closer to four percent, but let's not be picky). We know this from a variety of independent measurements, including the results of nucleosynthesis in the Big Bang, measurements of temperature fluctuations in the cosmic microwave background, and (less precisely) by direct detection. Everything we have ever seen is only one-twentieth of everything there actually is.
This leaves 95% of the universe as stuff which is completely invisible. As depicted, it comes in two components: 25% "dark matter" (in red) and 70% "dark energy" (in blue). The difference between the two is in how they behave: dark matter acts like ordinary particles, in that it collects into dense regions (like galaxies or clusters of galaxies), whereas dark energy is smoothly distributed throughout space and slowly-varying in time. The best candidate for dark energy is the cosmological constant, or "vacuum energy": the idea that there is a nonzero amount of energy density inherent in the fabric of spacetime itself.
Dark matter and dark energy are not theoretical constructs which were invented by cosmologists because they seemed interesting; observational data have forced us into positing their existence. Even though they are invisible, both dark matter and dark energy give rise to a gravitational field; we can feel their effects. Dark matter contributes to the total gravitational field of galaxies and clusters, which we measure by observing the velocities of nearby particles, or the deflection of light passing by. Dark energy is smoothly distributed, but affects the geometry of spacetime itself: it makes distant galaxies appear to accelerate away from us, and it "flattens" the geometry of space, two effects which have been directly observed. These dark components are exactly the opposite of the "ether" that was popular a century ago: everyone expected ether to exist but nobody could find evidence of it, whereas nobody expected dark matter or dark energy, but we found them despite ourselves.
Although this picture of a mostly-dark universe fits a wide variety of empirical data, at a deeper level it makes no sense to us. In particular, why are the amounts of ordinary matter, dark matter, and dark energy basically similar, when they could easily have been vastly different? This puzzle is especially acute for the dark energy as compared to the total matter (ordinary plus dark), since the matter density is diluted away as the universe expands, while the dark energy density remains close to constant. So the approximate coincidence we observe today between the amount of dark energy and the amount of matter is a short-lived one (cosmologically speaking) -- earlier on, the matter was dominating, and before too long (a few billion years) the dark energy will have completely taken over. The history of cosmology teaches us again and again that we do not live in a special place in the universe, but this state of affairs seems to be indicating that we live in a special time. (Personally I think it's probably just a coincidence, but there very well could be something more profound going on.)
For more discussion, see my Cosmology Primer, or my article "Dark Energy and the Preposterous Universe" (html, astro-ph/0107571), or slides from my related talk, or other discussions on my reviews page.