Quarks are always found bound together in hadrons (either mesons or baryons). They are bound by the strong force, which is mediated by "color charge" carrying gluons. Unlike the gravitational or electromagnetic forces, the strong force does not weaken with distance, which means it is really hard to pull quarks apart--they are always bound by a thin "tube" of gluons. However, once you add enough energy to the system to get the quarks sufficiently far apart, it becomes energetically favorable (meaning you've added enough mass-energy to the system) to create quark-antiquark pairs which bind to the separated quarks, thus producing new hadrons.

I recommend reading the linked Wikipedia article and its references.
Source(s):
http://en.wikipedia.org/wiki/Color_confinement

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