What about putting a toothpick or a stirring stick (the ones you use for coffee) and put it in the glasses on the table? You can put a tag on a ribbon with their names or a quote.
There was a project on making your own cherry blossom branches out of twigs and tissue paper in the Martha Stewart Weddings magazine (i think). It didn't look like it took a lot of time to make.
I've tried the chocolate bag idea before and find that it works better with wax paper. The brown bag didn't tear off very well. How about making a lantern with the brown paper bag? You can cut different shaped holes or pierce the paper with different patterns.
How about making envelopes out of them or covering a folder with it? Covering it with contact paper will probably keep the paper from fading and tearing.
My boyfriend's sister is a teacher and brings home tons of schoolwork, so maybe a nice canvas bag with her name or initials on it? Last year a student gave her a handpainted container which she now keeps on her desk for treats on special days. I agree with SNK725 that any gift from a student would be appreciated.
Maybe include a journal, definitely postcards/stationary WITH stamps on them, and a CD with her favorite songs if she brings a CD player. A big beach towel or cool pillowcase would be fun too.