In the windows-form world menu layouts are pretty settled, but no standard has emerged yet in the web-form world.
In a windows form try to keep your menus parallel to how Microsoft has theirs laid out: always a File menu at the farthest left, and a Help menu farthest right.
Use horizontal separator lines to partition out items of similar function, and be sure to enable hot-key shortcuts to the commonly used items. You should avoid a single item alone between separators. Menus shouldn't exceed eight or so items in any dimension (per pulldown or across) and shouldn't pop-out more than two deep, although I usually require a fairly serious reason for any pop-out after the first one.
Interfaces on web forms are tending toward an artificial "tabbed" approach. This works reasonably well provided you stay consistent with fonts, vertical spacing and presentation layout. More than three levels deep of tabs looks ridiculous; at that point its better to partition master pages into separate functional groupings. Avoid mixing horizontal and vertical menus on the same page and use a consistent menuing approach throughout your application.
Laying out menus is an art all its own. It's rather like playing rhythm guitar -- take the time to do it right and your menus should look good, be clean and intuitve, and stay in the background.
