rt-click on the window title and select one of the options to set the window size (I'm away from my Elive at the moment). One of them even gives the option to make windows for a particular app a certain size (1280x728 for example). For me the pdf viewer is the worst offender.
OK, rt-click on the title bar, go to More...--->Remember--> Size and Position. A more flexible solution could be to set a maximum size, matching the resolution of your screen (like 1440x900) found under More...--> Window Properties. If you have selected another option related to remembering size or position these options will be greyed out.
