Open Office is an open-source (free-to-use) word processing program that boasts tools and an interface similar to Microsoft Word. Unlike other free word processing programs, Open Office is fast, easy to install, and can save your files in a variety of formats (including .doc and RTF.) It also boasts an additional PDF-printing add-on that allows you to export your document direct from Open Office, thus preserving your pre-formatted text and images that may have otherwise not remained. Open Office's main downfall is that it can't format as properly as, say, Microsoft Word, but it works well enough, especially as a free alternative.
Similar to a word processing program but supplying all the extra bells and whistles that a detail-oriented writer could need, Y-Writer from SpaceJock Software allows users to be as detailed as they like. Whether you're a writer who takes detailed notes on scenes, characters and locations, or one who likes to add and rearrange scenes and chapters, Y-Writer allows you to do that, all from the comfort of one single window. Though the learning curve is steep even with the PDF guide, Y-Writer is a great program, especially for those who like to keep everything in one space.
Sonar, also from Spacejock Software, is a submission-tracking software that allows users to keep track of how long stories have been "out to market" and to which markets they've sent their stories. By simply adding the name of a story and the market the writer plans to submit to, Sonar can keep track of the story's time out from day one. The greatest thing about Sonar is its market-managing capabilities. If you haven't heard back from a market for a while, simply click the story, open the market details, then click on the "Go to site" button, which automatically takes you to the publisher's page. Sonar is a great, simple tool, one that every writer should have. However, you may want to keep a copy of your records in separate locations. A crash in Sonar can mean not only the loss of time frames, but the details of where your work has been submitted.