I hope this doesn't disqualify my advice, but I don't have kids. Having said that, I WAS a kid, and my mother kept giant cardboard folders of papers and drawings from my childhood. I think it isn't so much which ones you choose, as much as it is that you choose some. Years from now, you're going to love looking through them, and it will be special, and you won't remember the ones you didn't keep. I think it's a symbolic thing. Whatever you keep will be precious; there's no wrong choices.
A suggestion: for drawings and artwork: Put them all in one stack and quickly go through them putting them in a pile on your table. Any that stand out of any reason, set aside. Do it quickly, so your subconscious will take over. Another way might be to only keep drawings from holidays, special occasions, school events, etc.
For school work, pic a few for each subject (if there are subjects yet). Something on the alphabet, something with numbers, something with animals etc. I scrapbook, and I think what you are doing must be similar. I can't save EVERY special moment of my life in a book, so I just sort through and save ones that make me talk out loud (like if I find myself saying out loud "Oh, that's a good one!", etc). You can't save every moment, so just try to choose moments that represent many other moments, if that makes sense.
Hope that helps.