In this optical CCD frame, taken at Lick Observatory, the dark spots are clearly visible. In fact, these should now be visible through a 4-inch telescope with good image scale and atmospheric conditions.
Best assessment of the Damage
This image from the Hubble Space Telescope clearly shows the scale of the dark spots that have resulted from the impacts.
HST comparison of Violet and Ultraviolet Images of Dark Holes
The holes stand out, as expected, extremely well in the UV where all the surface features of Jupiter disappear. In the UV the holes appear rather large, rivalling the size of the Great Red Spot. It is not immediately clear why this should be the case but clearly the UV albedo of Jupiter has been greatly modified.
Near Infrared Brightnesses of the Holes
This image has a good deal of science in it has it represents a low resolution spectrum of the impact sites ACEFH which reveals a clear wavelength dependent brightess in the near IR. The contrast is best in the longest wavelength image as Jupiter is fairly dark there due to upper atmospheric absorption by methane. Since the fragements have literally punched a hole through Jupiter, then the methane absorption is locally reduced there (as it is at the poles).
True Color IR image (jpeg format)
High marks for aritistic impression here!