I'm generally a 'start at the beginning and work to the end' kinda writer, but the longer the story the more likely I'll get important 'later' scenes inspiration and need to get them down even if I'm not there yet.
For me, the best programme is OneNote. Yes, it's Microsoft. You can buy it on it's own or it comes as part of Office in most cases.
It is possible to use OneNote without buying it. Skydive can create an online version and it's free, plus you can then access the file wherever you are with an internet connection. The online version is not quite as good, but still has the all the basics which mean this is my favourite way to write.
It's not a story writing programme, it's an 'everything note taker/project maker' ... but I think it's perfect. You can open different groups (LnC fics, Smallville fics, Fairy Tales etc) within them you can start new files (Under the Spotlight, Waiting in Line, A Pirate Affair etc). Within each of those you can have as many pages as you want. I usually do a chapter to each page.
On each page you can type different scenes into different boxes and pick them up and move them around as much as you want.
I usually set up an info/research page for each story too. You can insert tables for timelines, draw, highlight, copy from the internet and it will insert a little hyperlink so you can always get back to where the information came from.
If using a version saved on SkyDrive you can invite other people to be authors and when they modify you can see the changes. This is extremely useful for joint projects or beta readers.
