A major new addition to WordPress 3.0 were custom menus. This gave you the ability to have full control over your menus, and removed the need for several plugins that performed various functions such as excluded pages from the menu, set pages to auto redirect to a custom link and my own page menu editor, which allows you to edit the menu label and title attribute to be different from the page title. It also removes the need for setting up ordering using the menu order option in the page attributes (and then deciding to insert another page and having to reorder all pages after it!).
Custom menus are so simple to set up with just a few lines of code needed to get started, and then you can make use of the Appearance -> Menus section within the admin. A simple drag and drop system which allows you to create menus consisting of page, post, category, custom post type, custom taxonomy and custom links. It's so much more flexible.
To get started with custom menus I recommend reading Justin Tadlock's tutorial which tells you everything you need to know – WordPress custom menus. Well, almost everything, there is one item missing from his tutorial (although it may have been added since I last read through it), which is how he has the CSS class, link relationship and description showing in his second screenshot. To get this you need to open up the screen options section up at the top of the screen and you'll see the extra boxes that you can tick to display (or not as the case may be).
We now use custom menus on every new site we set up, and we even use one for the site map as it makes more sense to do so. If you've not already started using them then I highly recommend learning and switching to them.