Poynter's website has a good post on 10 digital tools they feel can help improve reporting and storytelling.
Several are what I'd call research tools - FOIA Machine | (@FOIAMachine) (helps create and track FOIA requests); Census.IRE | (@IRE_NICAR) (search, organize and view 2010 Census data); iWitness | (@AdaptivePath) (curates social media, searchable by time and location).
However, most are storytelling resources; things that can provide background, graphics, and facilitate multimedia storytelling.
Public Insight Network | (@publicinsight) and Ushahidi | (@ushahidi) maintain databases of people eager to tell their story - although I'd worry about accuracy and bias in what is essentially advocacy.
Several help journalists create and develop graphics or incorporate multiple media forms into stories - TileMill | (@TileMill) (creates interactive maps); Tableau Public | (@tableau) (user friendly app for compiling graphs, charts, etc.); Popcorn Maker | (@mozilla) (adds interactive features to videos); Atavist | (@theatavist) (tool to compile elements into a single multimedia story, app, magazine, or ebook.
The final one is The PANDA Project | (@pandaproject), which allows newsrooms to share data and materials among reporters, and allows online collaboration.
I'll encourage you to check the Poynter post for more details, and examples of some of the ways media outlets have utilized the tools.
Source - 10 digital tools journalists can use to improve their reporting, storytelling, Poynter