Heavy quark physics serves as a probe to understand QCD, measure standard model parameters, and look for signs of new physics. We study several aspects of heavy quark systems in an effective field theory framework, including both phenomenological and formal applications. Phenomenological applications include the leading calculation of penguin amplitudes in charmless non-leptonic B-decays to light mesons, including power suppressed effects that are numerically enhanced by the chiral condensate. We compare our determination of the penguin amplitudes with the experimental results. Also, we calculate the heavy quark jet function at two loops, which is an important ingredient for the next-to-next-to-leading-log invariant-mass distribution of jets induced by tt pair production at a future linear collider. Formal applications include: a definition of top mass relevant for measurements that use top induced jets, a new renormalization group equation in an infrared scale intrinsic to heavy quark masses and its generalization for QCD matrix elements, a threshold mass definition which smoothly connects to the MS mass, and a new method to analyze renormalons in the operator product expansion.