I just did a quick Google scholar search to find the most frequently cited ISMIR paper. I'm not sure if I missed any, but it seems the most frequently cited paper is "Mel Frequency Cepstral Coefficients for Music Modeling" (PDF) presented in 2000 by Beth Logan. According to Google scholar it has been cited 127 times as of today. My coauthors and I have cited that paper several times :-)
MFCCs were originally developed in the speech processing community. Back in 2000 it wasn't obvious if the same techniques could just be "copied and pasted" to music information retrieval. MFCCs are now a very standard technique that are being used to compute music similarity, classify genres, identify instruments, segment music, ... In fact, today MFCCs are so common that they are often mentioned in ISMIR papers without citing a source.
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