Recently in the CCP4BB, there is an interesting thread with extensive discussions on "Citations in supplementary material". The original poster refers to the recent Acta Cryst D editorial with the same title in which the authors highlights the issue of under-citation to papers published in the International Union of Crystallography (IUCr) journals.
The main point is that method papers are more likely to be cited in the supplementary materials only, which are not indexed by PubMed, Scopus, Web of Science or Google Scholar etc. As a result, they are statistically undercounted, and "Journals and scientists that focus on publishing methodologically oriented papers are particularly affected." Specifically, through a survey of articles on protein or nucleic acid structure determination published in Cell, Nature, Science, and PNAS in 2009, the authors found that "almost half of all references to publications in IUCr journals end up being published in the supplementary material only."
The findings of the editorial resonate with my observations, and I cannot agree more with the authors that "in the end, methods need to be continuously developed and refined in order to ensure progress."
On the other end of the spectrum, some highly influential method papers are heavily cited. As an extreme case, the large number of citations to the 2008 paper "A short history of SHELX" by George Sheldrick helps rocket up the impact factor of Acta Crystallographica A by 20-fold to 49.9 this year!