I keep a grimoire of stuff concentrated in a Word doc. That's where most of my info goes. Then, I have a single text file where I write down various small ideas, which is generally snippets of dialogue, a chapter idea or a scene.
My Word doc is my baby though. I keep it neatly organized as I can (well with lots of TODO notes) so the navigation sidebar looks nice... （´＿｀）And so my writer can actually find shit! It pretty much has all info about the world in it.
Doesn't that look nice? I'm way too into aesthetics of a sidebar. But, that's how I organize my stuff.
My actual concept art though is all over the place. It sits in my general art folder with the 5000 pieces I've done. Not good with that. I've recently started to organize my character design folders so I'm getting there.
Sketchbooks, notebooks, word documents (and everything digital is on dropbox as well as external hard disks).
I think it's smart for creators to make sure to write things down and have all that kind of information stored elsewhere than just your own head. If you should be very unfortunate and end up in an accident of some sort that would do serious damage to your head, you could be at risk of losing that information. You would probably have bigger worries if something like that happened of course, but it's nice to know that at the very least I have a copy of all comic-related information safely stored outside my brain, so I don't risk losing it forever if something should happen. Not that you should walk around and constantly worry about hitting your head though 
I am curently in the making of a book that contains all the information on the world of Stormspectrum, divided in races, countries, laws, foliage etc. Along with that there are pictures to explain everything. It has a index and all, so if I need something but can't remember it from the top of my head, I search in The World of Stormspectrum. Wich I constantly add stuff to.
It's all in my head. Have tried writing the world info out as a supplement for my players for Pathfinder. It's far more organized in my head.
I record ideas i need to keep in mind, but I'm not neat or tidy about it in any way xD I literally have a libre office filed called "time gate shit" that just has a list of things I don't want myself to forget to do as I progress the story (just important events and interactions that I may or may not forget about). When I'm not in "time gate shit", I just track quick thoughts and ideas in Notepad, then move them to the libre office file where I save the ideas if they're good enough xD
I chew it up then spit it out all over the page. Funny you ask. I'm working on a huge idea right now. So huge that I filled an 80 page notebook with lore.
I use google sites to organize my lore. (Partially because I needed to be able to share it with others and didn't know of any other free ways to do it that easily, buuut.....)
https://sites.google.com/site/adestria2/29 is the site. Feel free to look through and see if it looks like something you could do easily
I have a jillion word documents filled with notes...it's not very organized but I guess it's worked for me so far. I also have a weird self-socratic seminar file where I list what I know about my world's "lore" and what I need to elaborate on. For example, "Character A does X. But WHY do they do that? Because character B stole their lunch money? That doesn't make sense! You're right. They probably did it because 10 years ago, Character C did blah blah blah" and in this way I flesh out character and plot in a way that informs each other. I nail down the specifics when I do the scripting. I have notes in every medium though--on napkins, in notebooks, on my digital doodles. Everywhere. I'm not very organized >.< but I never have been. I also spend every night thinking through/about my story as I fall asleep. The idea for my comic came from a dream, so I figure my subconscious has all the answers I need.
SCRIVENER18 is the way to go. Such a great writing program that packs a punch.
if u want to do the job as a badass.. go with dreamweaver! u have to do all by yourself, but u can do as u want. and then, u have everythin as u want. if u have not the html skill (& patience!) u can try Scrivener.
(both are NOT freeware)
ps: there re many freeware software like dreamweaver. pick your best.
for a freeware version of Scrivener, there re not good news. alll the programs i tried was quite bad.
an alternative, it s to "draw" your story. in PS or similar.
im doing a big file "*.TIFF" with alll the connection draw on the storyline like in the story. it help, but it s to easy to do a mess.
I don't use a specific program but I have different files for every thing. I used a character creation template12 to help develop characters then I store all of the characters info in a file for them. Anything involving that character goes in there (sketches, lore, etc).
Then all of my individual character files are put into a file labeled "characters"
All of my story writing is in a "Story" file
All of my reference pictures are in "Reference pictures" in different files. I organize those by different locations (I use real places in my story so I organize by city so I don't get confused) or by what they are (like clothing and what not).
page originals are in a different file than finished pages which are in a different file than the pages for tapastic (I have to shrink them to post them here).
All of these files are stored in yet another file labeled by the comic's title.
Long story short, File-ception the crap out of it.
If I'm passionate enough about a concept, it'll be my life. No need to organize it, no need to write it down. My mind will explore it on its own and come back to me later with its findings. Those findings I then use to create a story. I don't like to explain concepts to anyone because if you are en media res, no character is going to explain anything to you. It should be life to both you and your character. Once its life, there's no need to even think how everything works. It just does.
google drive. google drive for all the things (except for actual pages, those go in the external HD)
for keeping track of order of plot events, Twine is a pretty good way to go. it's normally used for creating branching text adventures, and because of that the format of the program is like putting sticky notes on a wall. which is what i used to do, until the sticky notes started falling off. :B
and Evernote's pretty fancy. you can have notes in different notebooks and add tags to them. they can be used to keep scripts and character notes.
if you use Windows, then yWriter is amazing for organizing chapters, scenes, props, and characters. but i had a friend whose yWriter files got corrupted, so... be sure you keep a backup for your story in case that happens.
I also have a cheap pad of paper where thumbnails and scripts and character notes are jotted down on the same page and over each other -- the mad clutter somehow feeds the brainstorm -- but i don't recommend relying on that haha.