I consider my 2008 paper “A critical re-appraisal of the obligate scavenging hypothesis for Tyrannosaurus rex and other tyrant dinosaurs” to have the highest “underappreciated:applicability” index. (The fact that it took 10 years for the paper to actually come out doesn’t help my appreciation for its unappreciatedness, too…)
It isn’t that other theropod workers ignore it; they do cite it. But since the topic of tyrannosaurid predation is studied by a larger spectrum of workers, many of whom do not have particular expertise in dinosaur morphology or even paleontology, many papers where it SHOULD have been cited do not do so. This is particularly frustrating because it is not a hard reference to find on a scholar.google search, and more importantly because it was specifically written to be accessible to a non-specialist audience. Of course I don’t think that they had to agree with every point in it, but I did collect and address all the major arguments for obligate scavenging in tyrannosaurs proposed up to that point, so it should at least be discussed.
Furthermore, when (often younger) paleontologists respond to the newer (and sometimes non-paleontologically-informed) studies on tyrannosaur predation, they wind up “re-inventing the wheel” (not being aware of my paper from so long ago…)
Holtz, T.R., Jr. 2008. A critical re-appraisal of the obligate scavenging hypothesis for Tyrannosaurus rex and other tyrant dinosaurs. Pp. 370-396, in P. Larson and K. Carpenter (eds.), Tyrannosaurus rex: The Tyrant King. Indiana University Press.
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In my opinion, one of the least appreciated papers in dinosaur paleontology is
Janis & Carrano’s 1991 work comparing reproductive turnover in dinosaurs and mammals. The implications for this paper reach into nearly every aspect of dinosaurian ecology (size; evolutionary turnover rates; ontogenetic niche shifts; number of species per fauna; extinction sensitivity; etc.) in comparison to placental mammal ecology. And yet it seems (at least to me) to be underreported relative to its applicability.
Janis, C.M. & M. Carrano. Scaling of reproductive turnover in archosaurs and mammals: why are large terrestrial mammals so rare? Annales Zoologici Fennici 28: 201-216.
Dave Hone's Archosaur Musings 
The 2008 paper reflects what was known on this topic only down to ’98? No wonder it’s “unappreciated”–while the evidence for predatory tyrannosaurs was ample back then, some great new evidence has come to light more recently.
Only, not really. There really hasn’t been terribly much new in terms of types of evidence (although a few new exemplars are know), despite media hype to the contrary. For instance, already known at the time were specimens with bite marks from tyrannosaurs which had been healed over, which is why when the news reports such as being “new ‘Rosetta stones’ of Science!” it is very frustrating.
True, K. Carpenter’s paper on bite marks in an DMNH Edmontosaurus came out a decade before ’98. But the case was surely clinched by the T. rex tooth embedded in a hadrosaur caudal. IIRC that was only a few years ago.
How I share your feelings. My most under appreciated papers are the ones I never got round to submitting. At least yours was only a decade late.
The fact that the paper is part of one of the “Life of the Past” volumes may have something to do with the lack of citations. I’ve heard other authors complain that papers they’ve submitted to such volumes end up not being as widely seen as papers they’ve submitted to traditional journals (unless I’ve misunderstood the nature of their complaints).
There would be some merit to that, but this paper comes out among the top three hits on scholar.google.com searches for “tyrannosaurus scavenger predator”. So I have to wonder if researchers are doing their do diligence in researching the topic in advance, rather than assuming no one has done the work and that they are the first.