There is a lot of controversy about what dark matter is, but couldn't some of the missing matter be contained in black holes? Once matter is in a black hole, it cannot be seen or measured, so it's unaccountable.
Once matter is in a black hole, it cannot be seen, but it's not really true to say that its effect cannot be measured. Black holes still exert a gravitational influence due to their mass, just like every other massive object in the Universe. This is how we actually discover and measure the mass of black holes: by watching their effect on the matter around them. For instance, the supermassive black hole at the center of the Milky Way galaxy is so strong gravitationally that the stars very near it orbit at a very, very high rate. Using this and the equations that describe the orbits of these stars, we can actually estimate the mass of the black hole.
We know that dark matter exists in galaxies because the rotation curve is flat at large distances from the center of the galaxy. A "rotation curve" is simply what it sounds like: a graph of how fast the "stuff" in a galaxy is rotating as a function of distance from the center. Gravity predicts that V = sqrt (GM/R). The "M" means all the mass that is interior to the radius R.
A rotation curve is flat when the velocity is constant. If you look at this equation, this means that M/R must also be constant. So that means that as we go farther and farther out in a galaxy, the mass is growing (a LOT) even though the starlight is falling off dramatically. There needs to be some matter that we don't see. A host of other cosmological observations also imply the existence of dark matter, and amazingly, they predict about the same amount!
What's important to realize about this is that our studies of dark matter don't just tell us that "it's out there somewhere"; when we study a galaxy, we learn something about the total distribution of matter within it. This means that we know the dark matter surrounds galaxies and is not a central object, like a black hole, within galaxies.
The problem with your idea is that black holes are nothing that special, gravitationally: they're just accretions of matter. They are centralized in the middle of the galaxy, and according to the laws of gravity, they can't pull very hard on stuff far out at the edge of a galaxy.
Edit by Michael Lam on September 14, 2015: Since black holes have mass, one hypothesis for dark matter was that it was made up of lots of massive astrophysical compact halo objects, or MACHOs. These would be compact objects that do not emit electromagnetically, such as black holes, dead (non-spinning) neutron stars, or old and cold white dwarfs (sometimes called black dwarfs). If lots of these objects existed in the right distribution in the halos of galaxies, it could explain the observed rotation curves. However, gravitationa microlensing observations have mostly ruled out the possibilty of MACHOs as the explanation for dark matter. The current leading dark matter candidate are known as weakly interacting massive particles (WIMPs).
This page was last updated on September 14, 2015.