Databases to store the contact information and status of your sources, as well as one to keep track of documents/records/data you are using for your reporting.
Databases to store the audio files and transcripts of all your interviews.
Nut graf — or at least a draft of it.
Your list of lingering questions (or just things you want to keep in the front of your mind).
My Central Tenets of Creating Good Journalism
Story pitch goes here.