I don't know if it's my favourite, but I'm limited in choices since I'm broke. I use ywriter to organise scenes, add characters and locations and such, but they are really lacking in features. I would really like to organise the scenes in a timeline, without them being reordered in the chapters as well (I don't want to write & post chronologically, I only want to keep an eye on what happens when for plot reasons). It's also impossible to not have a PoV character for a scene, or at least I haven't figured out how to create one without one, now that I'm writing 3rd person omniscient for a change.

For research, tentative plot structure and notes for the story, I usually use dokuwiki. It's useful if you have pieces of information that you need to fall back on for several fics, such as character profiles and to organise the information I've researched and what to research still with lots of interlinking.

And then I always do my writing in Word/Open Office/etc. and copypaste the relevant bits into the other two.