We present the results of extensive multi-waveband monitoring of the blazar 3C~279 between 1996 and 2007 at X-ray energies (2-10 keV), optical R band, and 14.5 GHz, as well as imaging with the Very Long Baseline Array (VLBA) at 43 GHz. In all bands the power spectral density corresponds to red noise that can be fit by a single power law over the sampled time scales. Variations in flux at all three wavebands are significantly correlated. The time delay between high and low frequency bands changes substantially on time scales of years. A major multi-frequency flare in 2001 coincided with a swing of the jet toward a more southerly direction, and in general the X-ray flux is modulated by changes in the position angle of the jet near the core. The flux density in the core at 43 GHz--increases in which indicate the appearance of new superluminal knots--is significantly correlated with the X-ray flux. We decompose the X-ray and optical light curves into individual flares, finding that X-ray leads optical variations (XO) in 6 flares, the reverse occurs in 3 flares (OX), and there is essentially zero lag in 4 flares. Upon comparing theoretical expectations with the data, we conclude that (1) XO flares can be explained by gradual acceleration of radiating electrons to the highest energies; (2) OX flares can result from either light-travel delays of the seed photons (synchrotron self-Compton scattering) or gradients in maximum electron energy behind shock fronts; and (3) events with similar X-ray and optical radiative energy output originate well upstream of the 43 GHz core, while those in which the optical radiative output dominates occur at or downstream of the core.
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