Dark energy and dark matter describe proposed solutions to as yet unresolved gravitational phenomena. So far as we know, the two are distinct.
Dark matter originates from our efforts to explain the observed mismatch between the gravitational mass and the luminous mass of galaxies and clusters of galaxies. The gravitational mass of an object is determined by measuring the velocity and radius of the orbits of its satellites, just as we can measure the mass of the sun using the velocity and radial distance of its planets. The luminous mass is determined by adding up all the light and converting that number to a mass based on our understanding of how stars shine. This mass-to-light comparison indicates that the energy in luminous matter contributes less than 1 percent of the average energy density of the universe.
There is certainly more matter in our galaxy and other galaxies that we cannot see, but other evidence indicates that there is an upper limit to the total amount of normal matter present in the universe. By normal matter, I mean stuff made out of atoms. Recently, NASAs Wilkinson Microwave Anisotropy Probe (WMAP) satellite made precision measurements of the imprint of sound waves on the cosmic microwave background, produced some 400,000 years after the big bang. Because sound propagation depends on the properties of the medium--as anyone who has played with a helium balloon knows--the pattern of the sound waves viewed by WMAP is an indicator of the abundance of hydrogen and helium in the universe. (All other elements were built from these basic building blocks.) These and other results agree with the theoretical predictions of the primordial abundances of the light elements as a result of the nuclear processes that took place in the first three minutes of the universe--also known as big bang nucleosynthesis. Ultimately, very strong arguments have been made that at most 5 percent of the mass-energy density of the universe, and 20 percent of the mass of clusters, is in the form of atoms.
What could dark matter be? Many physicists and astronomers think dark matter is probably a new particle that so far has eluded detection during particle accelerator experiments or discovery among cosmic rays. In order for a new particle to behave as dark matter, it must be heavy (probably heavier than a neutron) and weakly interacting with normal matter so that it does not easily lead to light-producing reactions. The prototypical dark matter candidate particle is something like a neutrino, though all known types of neutrinos are too light and too rare to explain dark matter.
How does dark matter affect the universe? The dark matter problem can also be viewed as a question of the nature of clustering matter. Dark matter must be the basic building block of the largest structures in the universe: galaxies and clusters. Without dark matter, the universe would be a very different place, according to current theories.
And dark matter is not just for explaining the behavior of distant bodies in the cosmos, but is abundant within our galaxy as well. It is estimated that our solar system is passing through a fine sea of dark matter particles with a density as high as roughly 105 per cubic meter. We may hope to detect the flux of dark matter passing though the Earth, and even to detect the seasons of dark matter, corresponding to the times of year when the Earth is moving with, or against, the flow of dark matter orbiting the center of the Milky Way.
Dark energy, on the other hand, originates from our efforts to understand the observed accelerated expansion of the universe. In a nutshell, current theory cannot explain the acceleration. One speculative possibility is that the acceleration is a consequence of another new form of matter, nicknamed dark energy, which has hitherto gone undetected. It is called "dark" because it must necessarily be very weakly interacting with regular matter--much like dark matter--and it is referred to as energy because one of the few things we are certain of is that it contributes nearly 70 percent of the total energy of the universe. If we can figure out what it really is, it is certain we will find a more illuminating name.
With the establishment of the big bang cosmological model, it had widely been expected that since the birth of the universe some 13.7 billion years ago, the cosmic expansion had been slowing down. But two independent research teams found in 1998 that the expansion was speeding up. If you consider that this expansion is the single most remarkable property of the universe as a whole, then the discovery of the acceleration is truly a breakthrough.
The acceleration is determined by measuring the relative sizes of the universe at different times. Specifically, astronomers measure the redshifted spectra of, and luminosity distances to, stellar explosions called type 1a supernovae. The time required for light from a supernova to reach our telescopes is encoded in the distance (the relation is slightly more complicated than distance = rate x time, due to the cosmic expansion), while the change in the size of the universe from explosion to observation stretches the wavelength of the emitted light, as characterized by the redshift. A comparison of these sizes at a sequence of times reveals that the universe is growing at an ever faster rate. Since this discovery measurements have improved and other cosmological phenomena, also sensitive to the rate of expansion, have been used to confirm these results. (One note: the expansion rate and the acceleration are not measured in meters per second and m/s2, respectively. Rather, they measure the rate of change in the dimensionless scale of the universe, and the second derivative thereof, so the units are 1/s and 1/s2.)
Einstein's theory of general relativity predicts that the cosmic acceleration is determined by the average energy density and pressure of all forms of matter and energy in the universe. Yet no known forms of matter can account for acceleration. Thus, something other than dark matter, atoms, light, etc., must be responsible. One leading hypothesis is that the universe is filled by a uniform sea of quantum zero point energy, which exerts a negative pressure, like a tension, causing spacetime to gravitationally repel itself. This stuff, sometimes referred to as a cosmological constant, was first introduced by Einstein in another context (something he later referred to as his greatest blunder), but that's another story.
How is dark energy affecting the universe today? It is responsible for the cosmic speeding, and international teams of astronomers are working to refine measurements of that acceleration. At stake is judgment on Einstein's greatest blunder (the cosmological constant), possible insight into the fundamental theory of nature (quantum gravity and the quantum state of the universe), and the fate of the universe (a Big Chill or a Big Rip?).
It is tempting to try to combine the explanations for dark matter and dark energy, but there are great differences between the two. Dark matter pulls and dark energy pushes. That is, dark matter is invoked to explain greater-than-expected gravitational attraction. In contrast, dark energy is invoked to explain weaker-than-expected, and in fact negative, gravitational attraction. Furthermore, the effects of dark matter are manifest on length scales roughly 10 megaparsecs and smaller, whereas dark energy appears only to be relevant on scales of roughly 1,000 megaparsecs or greater. Finally, it is important to question whether the dark matter and dark energy phenomena may have gravitational explanations. Perhaps the laws of gravitation differ from Einstein's theory. This is certainly a possibility, but so far general relativity has not failed a single test. And striking new views of clusters have revealed behavior that is inconsistent with a gravitational cure--meaning that dark matter really is there. We are left looking for new particles and fields to fill in the missing matter and energy.