Typesetting option that includes makeindex (TeX Live, TeXworks)

The pdfLaTeX + Makeindex + BibTeX option in MiKTeX TeXWorks calls a MiKTeX-only command-line tool called texify (manual pages). There are several tools that do (nearly) the same thing, such as latexmk, rubber and arara. Choose one, learn the command line options from its manual, and then in TexWorks, under Edit/Preferences/Typesetting, add the program to "Processing Tools".

Note that latexmk is a Perl script so it needs a Perl interpreter to run; Rubber is written in Python so you need Python installed if there is no pre-compiled exe(cutable). Arara has pre-packaged installer for Windows.

Regarding options, you will surely have to add $fullname, which is the TeXWorks way of substituting the filename, and something like -pdf to generate PDF instead of DVI.

You could do something as follows (Edit > Preferences > Typesetting > +):

Depending on the location of your installation, your .bat file would be something like:

"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\pdflatex.exe" %1 %2 %3
"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\bibtex.exe" %4
"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\makeindex.exe" %4
"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\pdflatex.exe" %1 %2 %3
"C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\pdflatex.exe" %1 %2 %3