If the fragments explode above the clouds, there should be enough light reflected from various Jovian satellites to take spectra of the explosions. Since the atmosphere of Jupiter contains very few heavier elements to contaminate the spectra, they could give a great deal of information about the composition of cometary solids. If the fragments explode below the clouds, then spectroscopy must wait until the impact sites rotate into view from Earth. By that time everything will have cooled a great deal, and the cometary component will have been diluted by mixing with the Jovian atmosphere, making such study difficult. In that case the Jovian material itself may prove of interest, with spectroscopic study giving new knowledge of Jupiter's deeper atmospheric composition.
It seems somewhat more certain that new knowledge of Jupiter's atmosphere will be obtained, even if predictions differ as to exactly what that new knowledge will be. There is nearly unanimous agreement that the impacts will cause observable changes in Jupiter, at least locally at the impact sites. These may include changes in the visible appearance of the clouds, locally or more widely, measurable temperature fluctuations, again locally or more widely, composition changes caused by material brought up from below the clouds (if the fragments penetrate that deeply), and/or chemical reactions brought about by the thermal pulse and the introduction of cometary material. Any dynamic processes such as these will give a new and better understanding of the structure of Jupiter's atmosphere, perhaps of its motion as well as its static structure.
If sufficient material impacts Jupiter's rings or especially the ring satellites, then there should be local brightening caused by the increase in reflecting area due to the introduction of new material. These new ring particles will each take up their own orbits around Jupiter, gradually spreading out and causing local brightening followed by slow fading into the general ring background. Careful mapping of that brightening and fading will reveal a great deal about the structure and dynamics of the rings. Many believe that impacts on those small inner satellites are the source of the rings, the reason or their existence. Enhancement of the rings from Shoemaker-Levy 9 impacts would be strong confirmation of this idea. Similarly, the interaction of cometary dust with the magnetosphere and with the Io torus will be quite informative, if the dust density proves sufficient to cause observable effects. Radio telescopes will be active in the magnetospheric studies, along with optical spectroscopy of the ions and atoms in the torus.
Last, but far from least, the physics of the impact phenomena themselves, determined from the reflected light curves and from spectra, will be most instructive. Note the inability of scientists to agree on the level of Jupiter's atmosphere at which the terminal explosion will occur. (A few even believe that there will be no terminal explosion or that it will occur so deep in that atmosphere as to be completely unobservable.) Entry phenomena on this scale cannot be reproduced, even by nuclear fusion explosions, and have never before been observed. Better knowledge of the phenomena may allow scientists to predict more accurately just how serious could be the results of future impacts of various-sized bodies on Earth, as well as to determine their effects in the past as registered by the fossil record.