Hm, I think there have been a few topics like this around already, but I'll answer this anyway.
For me, organization is key. I'm the kind of person that has a million things going on all at once, so I *have* to organize myself. If you have Windows 7, you probably know about the "Sticky Notes" feature. Yeah, I've got tons of those all over my desktop to keep myself on track. My process goes like this - get an idea, write that idea down, think about if the idea is good enough (and possible) for me to make it into a VN, and then once I'm passed the idea stage, I design the characters & setting and outline the plot. Basically, I plan everything out, even things that may never be seen in the actual VN. It's easier for me to write according to a guideline for the scenes, so I do it that way. And, if I deviate from the guideline, I make note of that. Your web page idea is good, too, though. Whatever's easiest for you.
I either sketch out a diagram of the branches or use Microsoft Paint, so I can have a visual version of my outline that I can keep track of. After that, the writing phase starts. I write directly into Ren'Py. That way, I can lay out the code and leave #comments for myself throughout the script. It goes back to what I said: "for me, organization is key." Now, the BIGGEST mistake I made with my NaNoReNo project was that I didn't plan out the artwork as I was writing. Since I'm a writer who works with artists, I normally plan things out with them or have my free sprites already programmed in, but since I was my own artist, I didn't bother to plan anything out. Huge mistake. I drew a lot more than I had to because I didn't organize myself properly. My hands still hurt when I look at index cards...
The project I'm going to release next (In This Dream of Ours) went better for me than my NaNoReNo project. I had a general idea, made notes, wrote the whole thing into Ren'Py, found free art resources, coded in the art, found free music, coded in the music, and now I'm in the polishing stage where I'm adding some bonus features before I post it up. Much, much smoother.