Punctuated equilibrium operates, to a large extent, on a relatively low
scale-within or between species. Its main focus is the frequent pattern of
little or no change (stasis) over long intervals, punctuated by brief
periods of rapid change, in contrast to the standard Darwinian constant
gradual change. Some organisms show a more punctuated pattern, some more
gradual [possibly related to environmental conditions], but this does not
negate the presence of transitions.
The existence of known transitional forms closely matches the extent to
which a group has been studied and the extent to which it fossilizes. This
is the pattern that would be expected if most or all major groups evolved.
The denial of transitional forms seems to focus on those groups for which
there are good transitional forms (perhaps because they're popular with
pro- and anti-evolutionary folks alike). Demand fossil evidence for
evolution in nematodes, or sea squirts, or slugs, and you'll get no reply
except that there aren't enough fossils in the first place. However,
vertebrates have a decent fossil record and are popular. Thus, contrary to
Hamm (and Gish) there are primitive carnivores, plausibly ancestral to both
dogs and cats, in the fossil record. The drawing of a purported
"transitional" "fishibian" in Scott Huse's Collapse of Evolution doesn't
look all that different from the earliest amphibians, and when he asks
"where are the prized fossils with half scales and half feathers?", he
evidently does not realize that modern birds have scales on unfeathered
parts of the body.
New transitions keep turning up. I'm giving a talk in March on some
snails, including an undescribed species that is transitional between two
genera. Entemnotrochus has a long slit, open umbilicus, tall spire and
straight sides. Perotrochus (soon to be split) has a short slit, closed
umbilicus, lower spire, and round sides. My shell has a long slit, open
umbilicus, lower spire, and round sides. It's roughly in the right time
range for the transition, as well.