Let me preface by saying - you asked for it! I LOVE to talk about my binders.
I have two. A small one is for the road trip only. It has mapquest maps, a
AAA triptik from the website, information about rest stops and restaurants along the way, printouts of potential hotels to stay, and activities and ideas to do in the car. Also includes planning stuff like things to pack, shoes, custom t shirt ideas and artwork.
On to the BIG one:
I have a 3 inch binder. It is divided by a rainbow of pocket folders - red through purple. Each color is assigned to a topic or theme park.
The front page of the binder is the print-out of my original room reservation.
First (red)

section is All-Star Music information. Maps, tips and lists from threads or the DIS, photos, activities at the resort. A subdivider separates this section from all other resorts. This includes activities like Water Electrical Parade, , parking info, restaurant info and menus (i.e. Chef Mickey's, 1900 Park Faire, Boma). There are sub-dividers separating each topic that I use as needed.
Second (orange)

is general theme parks. This has info like pressed penny locations, GAC info, things that would apply to ANY park.
Third (yellow)

is Magic Kingdom. List of attractions we want to see, ride length, park hours, parade and fireworks times. Subdivider with printout of restaurant menus that we plan to or would like to eat at.
Fourth(green)

is AK. Same setup as MK section.
Fifth (blue)

is DHS. Same setup as MK section
Sixth (purple)

is Epcot. This is subdivided into Future World and World Showcase, then is setup same as MK section.
Seventh (white)

is Downtown Disney and Water Parks. Not much there, but some menus, park times, maps.
I bought something from ebay recently (an old hand-held video game that preceded Pal Mickey), and the seller sent me all of the current Disney individual park brochures, so I have each one in it's respective pocket folder.
I don't print out pages direct from the web, but copy and paste into a Word Processing document, so I can avoid printing ads and navigation stuff, and avoid duplication, like when the lunch and dinner menus are the same. Also my page breaks are good that way, and I can print on both sides of the paper.
I use standard 3 hole punch notebook paper that has the faint blue lines on it. They lines don't take away from the information, and all the paper is already punched, plus this time of year, you can get a hundred or 150 sheets for a quarter. Then you don't have to buy a 3 hole punch.
This is what works for me - I'm sure there are a million different ways to do it. I can't wait to hear what other people are doing.