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I'm using a master document by including the child documents with \include{} command. I can compile the master document to get the big document with all child documents included. I wonder how to get one big master document as well as individual child documents with the correct pagination through only one compile.

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I'm not sure what you are asking exactly. Is this about saving one run of pdflatex? Or about \includeonly to include only parts but get the page numbers right? – Christian May 2 '12 at 22:22
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Have a look at Keep chapter number of chapters inserted with \include which also takes care about page numbers. You need to recompile the document and set the chapter you want with \includeonly. There is no automated process yet, but just last week when I submitted my thesis I thought about writing a package for this. – Martin Scharrer♦ May 4 '12 at 20:28

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If you want just one compile (not multiple compiles with \includeonly for one child at a time) consider extracting from the full pdf. One of these might work for you: http://www.bloovis.com/wordpress/?p=241, http://www.angusj.com/pdftkb/#pdftkbuilder, http://multivalent.sourceforge.net/Tools/pdf/Split.html

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