Livescience examines the outer reaches of the solar system and finds a lot of rather interesting questions that we can't yet answer. First of all, Kyper Belt objects (the area of the solar system outside the orbit of the planet Neptune out to about 100 AUs) have a variety of colors, which indicate that their composition varies a great deal - far more so than the objects found in the asteroid belt, for example.
A very mysterious color labelled "ultra-red" matter exists on about half of all Kyper Belt objects and objects known as centaurs (KBOs that have recently moved between the orbits of Neptune and Jupiter). This matter is not found closer to the Sun, suggesting it is unstable at higher temperatures, and might even consist of organic molecules. We simply don't know right now what this stuff might be.
Another interesting item is that theoretical calculations seem to indicate there should be a LOT more stuff in the Kyper Belt. What happened to most of the objects out there? Over 99% of the mass that we think should be there - isn't. There are a couple of theories, or perhaps our best calculations are way out of line.
"One conjecture suggests when Saturn and Jupiter shifted their orbits roughly 4 billion years ago, their gravitational pulls slung Kuiper belt objects out of the solar system. Another says the Kuiper belt objects pulverized themselves to dust, which then was swept away by the sun's radiation."
Then there is the Oort cloud, which lies out even further - a fifth of the way to Alpha Centauri, our nearest solar neighbor, in fact, 100,000 AUs. We've never directly seen a Oort cloud object except the comets that come into our system from all directions, which infers the cloud is spherical, but there are also short period comets (like Halley's comet) whose orbits don't jibe with the Oort cloud being shaped like this - Halley's orbit around the Sun suggests there is an "inner" Oort cloud shaped like a doughnut.
There is also the rather contentious debate the scientific community has been having regarding planets that was kicked off by the discovery of large KBOs such as Eris and Sedna. Pluto wound up being "demoted" from a planet to a "dwarf" planet; the former asteroid Ceres and the recently discovered (by Caltech astronomer Mike Brown) Eris have joined it, but Brown and others think there may be as many as 200 other dwarves in the belt, and if you get out into the further reaches of the belt, 100 AUs or more, a object the size of Mars might be lurking around.
We still have alot to learn here on Earth as well, but a couple of future observatories might begin to shed some light on these questions. Two projects, Pan-STARRS (Panoramic Survey Telescope And Rapid Response System) and the LSST (Large Synoptic Survey Telescope) are being planned within the decade.