PDF seems to have become the standard for online distribution of publications, this is despite many obvious limitations. In particular from the point of view of chemists, any chemical structures no longer contain any chemical information. This means that for instance you can’t do a sub-structure search of PDF documents. Whilst Adobe Reader is the usual cross-platform viewer Apple provide there own PDF viewer called Preview. Preview employs Apple's implementation of Adobe's PDF specification, and uses of Apple's Cocoa graphical user interface, Quartz graphics layer, and QuickTime image codec. Originally developed for the NEXT operating system it has been improved and updated regularly by Apple.
There are now a number of applications for reference management but Preview can be used as the reader for references and here are a number of features that you might find useful.