What are the quantum mechanisms behind the emission and absorption of thermal radiation at and below room temperature? If the relevant quantum state transitions are molecular (stretching, flexing and spin changes) how come the thermal spectrum is continuous? What about substances (such as noble gases) which don't form molecules, how do they emit or absorb thermal radiation? Is there a semi-classical mechanism (with the EM field treated classically) and also a deeper explanation using the full apparatus of QFT?
The thermal radiation associated with some object is typically described in terms of the "black-body" spectrum for a given temperature, given by the Planck formula. This formula is based on an idealization of an object that absorbs all frequencies of radiation equally, but it works fairly well provided that the object whose thermal spectrum you're interested in studying doesn't have any transitions with resonant frequencies in the range of interest. As the typical energy scale of atomic and molecular transitions is somewhere around an eV, while the characteristic energy scale for "room temperature" is in the neighborhood of 1/40 eV, this generally isn't all that bad an assumption-- if you look in the vicinity of the peak of the blackbody spectrum for an object at room temperature, you generally find that the spectrum looks very much like a black-body spectrum.
How does this arise from the interaction between light of whatever frequency and a gas of atoms or molecules having discrete internal states? The thing to remember is that internal states of atoms and molecules aren't the only degree of freedom available to the systems-- there's also the center-of-mass motion of the atoms themselves, or the collective motion of groups of atoms.
The central idea involved with thermal radiation is that if you take a gas of atoms and confine it to a region of space containing some radiation field with some characteristic temperature, the atoms and the radiation will eventually come to some equilibrium in which the kinetic energy distribution of the atoms and the frequency spectrum of the radiation will have the same characteristic temperature. (The internal state distribution of the atoms will also have the same temperature, but if you're talking about room-temperature systems, there's too little thermal energy to make much difference in the thermal state distribution, so we'll ignore that.) This will come about through interactions between the atoms and the light, and most of these interactions will be non-resonant in nature. In terms of microscopic quantum processes, you would think of these as being Raman scattering events, where some of the photon energy goes into changing the motional state of the atom-- if you have cold atoms and hot photons, you'll get more scattering events that increase the atom's kinetic energy than ones that decrease it, so the average atomic KE will increase, and the average photon energy will decrease. (Or, in more fully quantum terms, the population of atoms will be moved up to higher-energy quantum states within the box, while the population of higher-energy photon modes will decrease.)
For thermal radiation in the room temperature regime, of course, the transitions in question are so far off-resonance that a Raman scattering for any individual atom with any particular photon will be phenomenally unlikely. Atoms are plentiful, though, and photons are even cheaper, so the total number of interactions for the sample as a whole can be quite large, and can bring both the atomic gas and the thermal radiation bath to equilibrium in time.
I've never seen a full QFT treatment of the subject, but that doesn't mean much. The basic idea of the equilibration of atoms with thermal radiation comes from Einstein in 1917, and there was a really good Physics Today article (PDF) by Dan Kleppner a few years back, talking about just how much is in those papers.
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Addressing only the question of how a continuous spectrum arises from what appears to be a set of discrete spectra associated with individual modes of interaction with a solid pahse material...
You can get a hint one of the things that is going on here by considering the Mössbauer effect. Individual photons are not required to interact with individual atoms, they can (and therefore sometimes will) interact with larger units of matter. IN the case of the Mössbauer effect they exchange momentum with a large unit of crystalline lattice rather than just the nucleus they interact with. You use the adjective "coherent" to distinguish these interactions.
The result is that a otherwise neat cluster of allowed energies is smeared out by the recoil associated with many different masses.
Nigel asks among other things if there is a semi-classical mechanism. This is an interesting point which has not been addressed so I am going to give it a try.
The classical equilibrium between the electromagnetic field and a harmonic oscillator occurs when the energy per mode of the field is equal to the energy per mode of the oscillator. This is true classically and it is also true quantum mechanically. The real problem is that in a classical system of balls connected by springs, every mode gets the same energy no matter its frequency. This is true from the equipartition theorem which is based on maximizing entropy, and it is also true from a strictly mechanical argument of tracking collisions. This is the source of the ultraviolet catastrophe.
One can evade the ultraviolet catstrophe in an ad hoc manner by restricting the mode energies of the higher frequency e-m field components. Planck's formula is usually explained this way. But a reading of Planck's paper shows that he really solved the problem by redefining the way entropy is calculated for an oscillator. Applying this entropy calculation directly to the electromagnetic field gives the desired results. But one could just as well apply the entropy calculation to the purely mechanical system. If one does, it turns out that the higher frequency oscillators are not excited to the extent one would expect from analyzing them as classical billiard balls connected by springs. The very high frequency oscillations are suppressed. If one then allows the oscillators to carry a small amount of charge, and calculates the resulting radiation according to the classical laws of antenna theory, it turns out you get the correct black-body spectrum.
The system breaks down if you allow two or three high-frequency oscillators with the properties of a classical billiard ball on a spring to be added to the system. They will quickly equilibrate with the rest of the gas in terms of x,y and z velocities; and once the do this, they will share this energy with their oscillatory mode as well. It is the laws of quantum mechanics that forbid the existence of such oscillators, thereby preserving the thermal equilibrium.
EDIT: I've posted a series of calculations starting here showing how you get the correct thermal radiation by looking at the moving charges in a quantum-mechanical system and calculating the radiation classically using the Larmor formula.