This might sound odd but I would find it fun if byond had a quiz that told you where you could approve on. Quizzes would give people who were learning something to do and would probably increase traffic.
Idea comes from http://www.byond.com/developer/ forum/?action=message_compose&parent=729136&forum=7
Maybe giving a menu item under help that says "Command Help" that links to the reference for those that don't know what a reference is or just look under help first(after all when someone needs help they generally look under help). Also adding "Developer How-To" and "Code Problems" under that menu.
Also adding a list of dream maker's hot-keys at the top of the reference(Or at least somewhere in it).(Like F1 to open the reference in dream maker?)
Opening the guide on first use of dream maker would help, Along with adding it under the help menu in dream maker.
Right clicking on the Lib folder could show a menu that says "Find Libs" on it taking them to the resources
Automatic folder seperation of file types(Option)
A start on start-up option for both the pager and dream daemon.
Also instead of a drop down menu for the new menu's types it could have a picture of each type along with the ability to type in your own type (Txt,html,ect) and the ability to add a file from outside of your project without leaving it.