Structured document processors (i.e.free alternatives to Scientific Word and raw TeX):
LyX combines the power and flexibility of LaTeX with the ease of use of a graphical interface; this results in world-class support for creation of mathematical content (via a fully integrated equation editor) and structured documents like academic articles, theses, and books. The Windows version can be obtained directly from here.
GNU TeXmacs is a free wysiwyw (what you see is what you want) editing platform with special features for scientists. The software aims to provide a unified and user friendly framework for editing structured documents with different types of content (text, graphics, mathematics, interactive content, etc.).
Excel2LaTeX allows you to write a table in Excel and export the current selection as LaTeX markup which can be pasted into an existing LaTeX document, or exported to a file and included via the input command.
Bibliographic software:
JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef is a desktop application and runs on the Java VM. Bibliographies generated by LaTeX and BibTeX from a BibTeX file can be formatted to suit any reference list specifications through the use of different BibTeX and BibLaTeX style files.
Mathematical and statistical software:
Gretl Is a software package for econometric analysis. It is free, open-source software. The name is an acronym for Gnu Regression, Econometrics and Time-series Library. It has a graphical user interface and can be used together with TRAMO/SEATS, R, Stata, Python, Octave, Ox and Julia.
Euler Math Toolbox is a powerful math program combining numerical and symbolic tools (using the computer algebra system Maxima) in one free package. It is quite similar to Matlab, but not compatible. The main design goal was to create a clean and simple surface that gives easy access to powerful tools.