This script moves all entries tagged with @done in the current project to the end of the current projects list of entries.

tell application "TaskPaper"
    tell front document
        set p to containing project of selected entry
        set move_entry_ids to {}
        set done_entry_ids to {}
        repeat with each in entries of p
            if exists (tag named "done" of each) then
                set done_entry_ids to done_entry_ids & id of each
                set move_entry_ids to move_entry_ids & done_entry_ids
                set done_entry_ids to {}
            end if
        end repeat
        repeat with each in move_entry_ids
            move entry id each to end of entries of p
        end repeat
    end tell
end tell