While most of the papers cited below examine BOTH physical and biological variability, I have tried to classify them on the basis of the main focus of the work.  Thus, biological papers are generally reporting an ecologic response to interdecadal climate variability, while climate papers mainly focus on the climate variability itself.  The statistical methodology papers mainly deal  with methods used in retrospective analyses of climate, biological populations and the relationship between the two.
 

Biological Papers

Climate Papers

Statistical Methods Papers

 

In addition to these lists, here are some additional collection of references that might be of interest

Publications by Fisheries Oceanography Coordinated Investigations (FOCI) scientists
Publications by Pacific Fisheries Environmental (PFEG) scientists
Publications by Joint Institute of the Study of the Atmosphere and Ocean (JISAO) scientists
Suggested readings as background for the GLOBEC Science Plan
Suggested readings on El Nino and Climate Prediction
Pan American Climate Studies (PACS) - Bibliography