Clipmark

NoteTab Light — Free Version — I built this web site with this program (every single incarnation of this site, including the current version, stylesheets and all).
Go to the NoteTab website.
Sonar — Free (donations accepted) — Created by the creator of yWriter, this handy program tracks submissions better than a spreadsheet.
Go to the Sonar website.
EverNote — Freeware — EverNote is a fantastic notekeeping program that makes keeping up with notes and research for multiple projects an absolute breeze. Highly recommended for all writers. More of my comments on Evernote.
Go to the EverNote website.
WordWeb — Free Version — WordWeb is a thesaurus and dictionary that can integrate with other programs or run as a standalone program.
Go to the WordWeb website.
RoughDraft — Freeware — RoughDraft is an easy to use word processing program created specifically for writers with features that meet a writer's unique needs.
Go to the RoughDraft website.
Similar programs: WriteWay, yWriter
TreePad Lite — Freeware — Great for notes, detailed lists, character and scene sketches, or just anything at all. I've created a story note organizer for TreePad. It's a simple document in the TreePad format that can be used as a template to help you organize all those documents that invariably accumulate as you work on your most recent novel(s). It also lets you keep track of submissions and rejections. Download my template story_note_organizer.hjt (right click and choose "save target as" or "save link as").
Go to the TreePad website.