Adjacency lists are in use in the sources I have found. For very large data sizes you might end up either holding the data on disk or using multiple machines to solve the problem - so I suggest adding keywords such as "external memory" or Hadoop to the search. I tried adding Hadoop and found some papers on solving single source shortest path via parallel breadth first search - http://www.cs.kent.edu/~jin/Cloud12Spring/GraphAlgorithms.pptx, http://courses.cs.washington.edu/courses/cse490h/08au/lectures/algorithms.pdf, Hadoop MapReduce implementation of shortest PATH in a graph, not just the distance
In addition, http://researcher.watson.ibm.com/researcher/files/us-heq/Large%20Scale%20Graph%20Processing%20with%20Apache%20Giraph.pdf does not cover shortest path but is an interesting example of solving connected components using a layer on top of Hadoop that may make life easier.