Medvedev P, Stanciu M, Brudno M.
Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009 Nov;6(11 Suppl):S13-20.
http://www.cs.toronto.edu/~brudno/nmeth_review09.pdf
A good 2009 review article on the state of paired-end sequencing. Includes some discussion of the difference between mate-pair and paired-end reads, the many types of of contig linkages they can produce, as well as discussion about data prossessing and available tools.