I scrapbook (when time allows) and the way I organize my photos is by years. I do a separate album though for Christmas. That is a fun one for the girls to go through and see how they have grown over the years.
If we have a big special vacation (like when we went to Alaska or Hawaii) I do a separate one for that trip.
Otherwise everything goes in the album for that year.
The extra photos I don't use go into one of those photo boxes. Then when the girls need a picture for their own projects they can find one.
I don't use film anymore, so I have lots of digital pics on my computer. I use Picassa (it's a free download from google I think) to organize all my photos. It will even find pictures on your computer that you didn't know you had. It's awesome. One warning...be sure to download your pictures to back them up. there are some good online places that will do it or download them by year onto cd's or a flash drive. Picassa allows you to group them into folders so it's really easy!
Hope this helps!