I'm barely 140 lines of code and maybe 1600 words into my first project, and I'm already starting to lose trail :-)

Right in the beginning, my protagonist comes across an obstacle and gets 3 different ways of dealing with it. Two of them give him another 2 or 3 choices, followed by even more choices within... How do you keep track of all that? Do you use any cool software to make sure all nodes are connected? Do you have a cork board with notes? Do you write your story in parts (as separate squiffy projects), test them separately, and then combine with the rest, if everything works? (clicking through the whole story is... painful; a back button or an option to start testing your story from a certain place would be nice).

The best advice I can give is before you do anything else make an "Extended StringList" in Word or something to that effect and write down, every single variable that has to do with your main character (or characters). For example, I have this...

player.haircolor: brunette 0, white 1, red 2, black 3, dirty blonde 4, platinum blonde 5, green 6, purple 7, dark red 8, orange 9, blue 10, ombre 11, neon 12, pastel 13, pink 14, silver 15, rainbow 16.

player.hairlength: bald 0, buzzed 1, short 2, shoulder length 3, long 4, very long 5, extremely long 6, dragging on the ground long 7.
{if player.hairlength_as_int>=1:}

That way, you never lose track of your variables.

Next, keep "sections" or "chapters" clustered together. Like...

Part 1
------- Starting Room
------- Room Stuff Happens
------- Room Stuff Happens
------- Room Stuff Happens

Part 2
-------Starting Room
-------Room Stuff Happens
etc

....And finally, I recommend Notepad++ --- it's free software that you can plug code directly into. It's also handy for large edits. If you need anymore advice lemme know!

Free writing software: ywriter6 by Spacejock Software. :)

You create a chapter such as Book One. Then you can create a scene (scenario) inside that chapter. You can create multiple scenes. Right now, I have named 100 scenarios, even though I have only written 25.

You can actually write all your text in a scene and then cut and paste that into Squiffy. Each scene has a tab which allows you to add detail. In the detail tab I write where the scene will lead to and what I plan to happen there. I then go to the scene that the choices lead to and make notes in the details of how the story arrived there, and what I am planning to have happen.

Excel. Just do scenes on the horizontal, depth in the vertical. This way, you can color the cells to show if you are complete or not. So, you might have...

Enter Mill
Open Door | Go through Window | Climb millwheel

I've had very extensive collections of mappings, and refer to them often.

I use Trizbort, its an interactive fiction mapper that have I've found useful for story development. I'm more of a visual learner so it works really well for me.

Maybe I'm old fashioned but I took a pencil and paper drew out a flow chart with each possible branch of the story.

Stacks and stacks of paper notes...
Maps...
Planed actions, ideas, and "didn't work" lists...
I think paper is easer than on PC... unless you have multiple monitors...
Altho, I do like the Excel idea!

Ha! You don't! That's the beauty of it. You just get lost in the sea of confusion forever and ever, while never actually completeling your game. =p

I actually had the same problem. I had wrote everything down on paper, but after intersecting and branching paths back and forth and making blank pages by mistake on Quest and losing track of other pages, I put my game on hold. Perhaps I could use the suggestions here as well. =D

each of the pages I make for the choices are given names that are the same as the choices. For example, if my choices for a page are:
she walked into a tree
she tripped over a vine
she laughed loudly
she tossed a water balloon at him

then the pages for those choices will be name:
walked into tree
tripped over vine
laughed loudly
tossed water balloon

They show up on the left side of the tree and the names let me know what's supposed to happen on the page.

I edit them in order they are in the tree, referring back to the page that linked to them to find out what happened there. Then, as I finish with them, I drag each one up and drop it on the first page - so that the first page becomes the parent. That let's me close the first page and its children, getting them out of the way.

Also, when editing each page, I make sure I give it a slightly generic description so that if I want to, I can link other pages to it and not have it sound like it's out of place.

The alternative is a lot of index cards for gamebook stuff and a lot of hex or grid paper with maps for text adventure stuff.

Flow Charts help, but sometimes, I just wing it.