I printed mine out on 4x6 blank index cards and left a white border around the images. Here is a pic:
Then I got a photo album and slid all of the cards in their own pocket. I would definitely suggest organizing them by alphabet so that you can easily find the character's card as you see them.
I made about 248 character cards and had a 250 card photo album that I carried around. Luckily I have a two year old and could throw it in the bottom of the stroller...otherwise, it could get a little heavy in a backpack if you are carrying a bunch of other things around. I was at WDW for three days in December (when school was not out) and got 48 signatures. We were there first thing in the morning when the parks were open and generally left around 2:00 in the afternoon for my 2 year old. The lines were relatively small for autographs because school wasn't out yet, which I think is why we were able to get so many autographs. We didn't go out of our way to get them. We just got them as we were on our way to rides or shows if we happened to see a character and the line wasn't too long.
You could just print cards for your favorite characters that you want to meet and then generic cards for other characters that you happen to see. It is up to you.
Other people leave either an extra large white border along the top or left hand side of the autograph card and then take all of the cards to "Kinkos" or a similar store and have them spiral bound. I like mine in photo albums so that I can pull out the signed cards and then use them in scrapbooks. It is up to you!
Here are some links to my favorite autograph cards:
Penny (Chaoscent)
http://s226.photobucket.com/albums/dd181/Chaos1Cent/?start=0
LJCollins
http://s345.photobucket.com/albums/p379/ljcollins_2008/
The above links require a good bit of ink...but are sooo worth it! Some people save the images to their "my pictures" and then copy them at Wal-Mart or wherever you get your photographs developed. If you do this, I would suggest printing them on matte photo paper. The only ones that you will have a problem with are the few characters that use stamps for their autographs. If you get theirs...make sure they are completely dry before you touch them or put them back in the autograph book.
If you are looking for some great autograph cards that require less ink...look in Natalie's file:
http://www.4shared.com/dir/5978989/a06aa930/Natalies_DISigns.html
Hope this helps!