As you no doubt know by now, there's a lot that can be done with JWM by editing .jwmrc-tray. I set it to limit the width of the application boxes displayed in the tray, gave it a "start" button with a custom menu distinct from the right-click menu (complete with sub-menus) and (since I'm not too concerned about tray real estate) I had it "swallow" the mount tool.
The joewing.net web site provides loads of useful information on JWM.