• Use common fonts: Sure, it's cool that you downloaded SuperKeen ExtraBold for free, and it's certainly spiffy looking. But will the Windows machine in your classroom have it installed? Don't bet on it. When you're building a presentation that will be shown anywhere other than on the machine where you're building it, stick with the safe list: Arial, Comic Sans, Courier, Courier New, Georgia, Helvetica, Tahoma, Times, Times New Roman, Trebuchet MS, and Verdana. Generally, these fonts will exist on any machine with a copy of Office installed.
• Use safe image and audio formats: Though the PowerPoint for Mac can interpret most PC image formats, the reverse is not true -- using Mac-specific images in a presentation destined for a Windows machine can bring you a world of pain. The problem becomes even knottier when you consider formats like TIFF that exist on both platforms, but have platform-specific features that inhibit proper translation. The safe list for image formats is short: PNG (Portable Network Graphics), JPEG (Joint Photographic Experts Group) and, for low-quality images, GIF (Graphics Interchange Format). Stick with these formats (in that order of preference), and you'll stay out of trouble. Same goes for audio -- keep sound in MP3 format for cross-platform serenity.
• Name your files properly: On the machine where your presentation is created, metadata in the presentation file generally allow the system to correctly tell what kind of file it is, and what program (PowerPoint) to open it with. Moving the file between machines, though, often strips this metadata, and leaves the destination machine giving you the computer equivalent of a blank stare that says "What is this thing, and what do you expect me to do with it?" Forewarned is forearmed -- name your files with correct extensions so that all operating systems can tell what they are. For Office 2003 and earlier (Windows) and Office 2004 and earlier (Mac), use .PPT as the extension. For Office 2007 (Windows) and the forthcoming Office 2008 (Mac), use .PPTX on presentation filenames.
• Don't embed files: PowerPoint for Windows enables you to embed documents from other Office programs -- Word files, Excel tables and so on. These embedded items usually don't translate well to the Mac. Avoid doing this.
• Stick with basic transitions and avoid animation: Certain fancy transitions do not move well from one platform to another, and the animation tools are different on each platform. Keep your transitions basic and two-dimensional, and avoid anything more than basic animations.

There are more tips to be found, of course, but following this short list of basic cautions will keep you out of trouble when moving PowerPoint presentations between Mac OS and Windows.

(Thanks to Indezine and PPTFAQ for great info on this topic.)