Here's my dear notebook (just look at those tapes), in which I design maps, minigames and characters. Other plans are usually writen on computer, and not all minigames even get here. For example cardgames, they're so self explanatory I only need to figure out in which order I start to create classes in the code and such.
There are some random drawings too and a few plans for changes in interface (which have been made to the game so don't expect changes).
Here's what my character design pages look like. Personality, history and motives are on my computer, so here I design their looks. I'm not much of a drawer, and considering I've been using this notebook for two years, it's funny to notice how much better my drawing style has gotten. These are one of my first designs. Currently I have 70 character looks designed.
After I've done the design, and I get to a part in the game where I need a picture for the character, I take A4 sheet and draw the character's upper part of the body (taking about half of the sheet). If necessary, I will draw another character right next to it. Then I take a copy of it and I strengthen the important lines with marker. Then I take it to the scanner, use GIMP to add some colors and finally resize the character into a smaller one and then it's ready for the game.
This is what would look like my plan for maps. In this picture, there's two areas, other being still unfinished. The left one is actually in the game already.
Basically I just draw squares, fill them with stuff, and when I have to make it to the game, I use my home-made "level editor" to put the pieces together. GIMP is used to draw objects, backgrounds and characters.
One time I also used this to decide where people are put, but as of now, I just open the map in level editor, look for a good spot and put him/her there. Before that I obviously design on my computer how many people will be on the whole area. I also have to design their dialogues before actually adding people in the area, you never know if you can't figure out anything for someone to say.
And here's what looks like my todo-list. 1770 lines as of now by the way. In this file I give myself tasks, and when I complete them, I put an X to the box and a date and time next to the task's description. Sometimes there are subtasks and completion percent is included in task's name.
Then I have 6 other files. One is for character designs (1581 lines), one for the structure and plans for story (820 lines), one for the script (13252 lines), one for the level editor output (depends on map), one for designing people on each area and map (4344 lines) and the final file is for tutorials in the game (845 lines).
That's pretty much it. This is certainly just a peak, but hopefully it motivated someone to organize the development process. It's seriously really useful.