I've been looking at building such a piece of software but it is just in the pre-design stage and I have no idea when I will actually have time to work on it. Everyone seems to want a tool like this but a good one doesn't seem to exist. Until one does come along I'm afraid there isn't a great solution.
I've tried flash cards, excel, word documents, wiki type solutions, primitive ui's. The best I can suggest is that you use a parseable text document. Come up with a simple text based encoding scheme that allows you to quickly write scenes in that can also be used by a parser in your game engine to render those scenes.
For example:
C1:Cat
C2:Jackal
C3:The Hunter
1|Opening
The rain fell steadily along the cold city streets. [[Cat]] ran as fast as her legs could carry her into the darkness of the nearest alley.
--She was alone and scared.--2.1
--[[Jackal]] was just behind her urging her forward. --3.1
--No matter how fast she ran or how far she could never out run [[the hunter]].--4.1
2.1|Alone
The alley reeked of human waste and filth. Why did they ruin everything around them? Why did they hate her kind so much? She was so tired of being alone.
--[item:pendant] Her mothers pendant shone with a strange light. One [[Cat]] had never seen before. It seemed to be guiding her towards a barren patch of wall. -- 2.1.1
--A nearby door had been left a jar, perhaps at last she might find somewhere dry and warm to spend the night. -- 2.1.2
--It was too risky she had to push on maybe the rain would stop eventually. -- 2.1.3
?? He was asking about software that already exists for mapping interactive/branching dialogue. You're giving him programming environments he can use to "build GUI software"? 
