All good suggestions.
I echo the giant zippered binder. For DS, once paper entered the desk or locker, it was gone. The key was to ensure that every piece of paper went into the binder instead, and came home, every day. Like yours, there was no way any paper was going to be properly placed when received in a binder or duo-tang - and teachers often gave them things without holes and little pieces of paper, so the zipper is crucial - just jam it in and zip. Then each night he had to sit down and figure out what each piece was, what work was associated with it, update his to do list, and file what was done. (And yes, all this took place with a heck of a lot of harassment, erm, I mean supervision).
She has each subject color coded and has been good about placing the correct subjects within the right colors, but we don't have a spot for papers given out throughout the day.I will "suggest" that she create a new color for daily homework sheets, random papers to look at when she gets home and either do as homework or file as necessary.
(This binder actually had parts of the cover that could be written on with a special pen and wiped, which was actually useful for taking note of the occasional instruction - something he is very bad at taking note of).
Very cool!!! DD could write her homework on the top of the binder!!
Our particular binder had tabs for each class on one side, and an accordion on the other, We used tabs for filing things that were complete (but still current enough he might want to reference; otherwise we purged). The accordion tabs were one for "To hand in", one for "To do" (and one actually for his laptop). As per SaturnFan, we worked on building the key habit that every time he walked into a class, he would look in the "To hand in" section to see if there was anything there for that class. If he couldn't tell me what he had to do with a specific piece of paper (what, when, how), we'd put a big post-it note with those questions on it, and put it in the hand-in section as a reminder to ask that teacher for clarification the next day.
Another section to create - she needs a new system because the clipboard she used to hold all the homework was one of the items that was falling out of her arms. Post in notes are the best!!