Digital File, a database for investigative reporters and researchers

Haven't tried it myself, but Digital File costs about $45 and was recommended by a reporter on NICAR-L. It's for organizing investigations:

It is bases on Excel and runs on every PC and Mac. The database helps keeping track of an investigation. All steps are documented in a way that allows quick access and overview. The database contains contact info about sources, questions to ask, documents and (interview) notes, as well as a time tracker and expenses sheet. ‘After years of muddling in Word, this really is a solution!’

The creator is Luuk Sengers, a freelance investigative reporter and journalism lecturer in The Netherlands.