Our students aren't allowed to carry anything into the actual ceremony -- as someone else said, it would look like a "most special" contest. If they're not all going to look alike, why bother with the cap and gowns?
AFTER the ceremony, many families give their daughters small bouquets -- I'll definitely do that next year for my daughter. Something that'll look nice against her cap & gown colors. Or something in her college colors, whatever those may turn out to be.
Being a teacher, I go to graduation every year, and I have no memory of a boy walking around with flowers. I can't imagine the boys feel slighted; it doesn't seem manly to walk around with flowers.
I suppose you could do balloons instead, but -- at our school anyway -- they'd take them from you at the door (and rightly so) because they'd block other people's view of the stage.