A way to save an older presentation in the new format is to apply the Convert command in PowerPoint 2007. The effect is that PowerPoint does an "in place" replacement of the old presentation file, converting it to the new format. The file then no longer exists in the old format.
To use the command, you open the presentation, click the Microsoft Office Button , and click Convert.
More file types
With PowerPoint 2007, there are additional file types you can choose for saving a presentation. For example, there's a new type available for a presentation that contains macros. See the Quick Reference Card for more details.