I have a similar problem with my Year 5s and their pencils. I generally have to replace at least three every day because they keep disappearing. I observed one of the teachers at my school constantly saying 'lids on, pens down' when they were using them and apparantly they have been trained to do so automatically. Alternatively you could try what I do with the pencil situation i.e. no one leaves the room until I see that everyone has got a pencil and that it has gone back in the tray. They hate being late for break and lunch so it's starting to work.

 Label each pen with the childs name? Its then their responsibility? x

 If pens are named and they can't find their own, the loss of privilege of use of a whiteboard(and having to use pencil and paper instead) can be enough of a deterrent for some but the genuinely forgetful . . . .  have to put all their equipment in a clear plastic wallet and be handed in at the end of the session.

Or, something I did one year, give a reward at the end of each week to the tables that still all had a full compliment of equipment kept nicely. I think they all got a sweet from a jar, clear and kept in view to motivate. But this does mean only having exactly what is needed in each basket. So 6 handwriting pens, 6 pencils, 6 rulers, 1 rubber and 1 sharpener. 6 whiteboards, 6 whiteboard pens and 6 rubbers. No colouring pens or pencils as they cannot be monitored in the same way. Worked a treat.