MiKTeX 2.9 comes with both and they apparently do the same thing. I was wondering what the difference between them is (if any) and which one is preferable for large documents.
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Two things that come to my mind:
Latexmk requires Perl while texify is a native command line application.
texify can trigger the automatic-download for missing packages. I’m not sure if latexmk can trigger it too.
And as TeXworks is available within MiKTeX you have another option, although its focus is not the same as for texify or latexmk.
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*latex. – doncherry Dec 15 '11 at 13:46miktexconfiguration. As far as I know the auto-download is tied to the compiler, i.e.latexorpdflatexit does not matter how the compiler it invoked. Thus ifmiktexis setup to download packages thenlatexmk's call tolatexwill also cause a package download, in the same manner as just runninglatexfrom the command prompt would tricker the download. – daleif Dec 15 '11 at 14:14