Legend:
- Software I started using in 2012 in bold.
- Software I’ve been using for many years (old faithfuls) in italics.
Used daily:
- ConnectedText
- Natara Bonsai
- Outline 4D
- NoteTab
- VUE
- Freeplane
- EndNote
- Directory Opus
- WordExpander
- Direct Folders
- PureText
- ClipCache Pro
- WinSplit Revolution
- MLO
- SE-TrayMenu
- AppleWirelessKeyboard (script)
- PDF-XChange Viewer
- Mindsystems Amode V2
- ClicKey
- Fences
- Protopage
- iDoneThis
- MozyHome
- Waterfox
- Classic Shell
Used frequently (at least weekly):
- Nebulous Notes (iPad/iPod)
- Surfulater
- Linkman
- Dragon NaturallySpeaking
- PDF Expert (iPad/iPod)
- GoodReader (iPad/iPod)
- Passwords Plus (iPad/iPod/PC)
- Dropbox
Used occasionally but indispensable for specialist tasks:
- ABBYY Screenshot Reader
- JPEGView
- Greenshot
- ABBYY FineReader 11 Pro
- TreeSheets
- Scrivener for Windows
- Search Everything
- Allway Sync
- TeamViewer
- Copernic Desktop Search
- CarbonFin Outliner (iPad/iPod/PC)
- A-PDF Comment Collector
- Notability (iPad)
- SmartDraw
Would like to use more:
- BrainStorm
- RecentX
- Story Turbo
- AutoHotKey
Haven’t used much (but still on my favourite list):
- iThoughts (iPad)
- Noteliner
- WhizFolders Organizer Deluxe
Dr Andus's toolbox 
If you aren’t into your final stage, you might think of using a Drupal website as your outliner. I can send you a link so you can download a portable website into a folder (includes the server) and you have a look. We call it ScholarWriter. Drop me a line if you want one.
For your visitors reading this, it’s best to start using ScholarWriter early. It keeps all your notes, drafts and outlines in one place and eases the messy recursive bit that this blog talks about.