Runaway sound files. By default, PowerPoint refuses to embed sound files bigger than 100KB, it just remembers where to find them (this is called linking). This has the practical result that your sounds play just fine on your computer, but not when it actually matters. To fix this in PowerPoint 2002/3 before inserting any sounds, go to Tools > Options > General > Link sounds with file size greater than ___ KB. This works a little differently in PowerPoint 2007 or later. If you’ve already inserted all the big sound files, resign yourself to doing it again after fixing that setting. Sorry!
Colourblind audience? Colour is a powerful way to communicate, but about 8% of men are colourblind (only 0.4% of women) — so if you want complete comprehension from an audience of more than 12 men, this matters. Red/green/brown distinctions are the hardest, but strong saturation apparently helps (pure and intense, not mixed with grey). Aim for redundant cues like dark/light contrasts or shapes and dashed lines. Blue is safe, hence the Facebook colour scheme. See what colour-deficient people see.
Print is in your future. Taking the colour issue a bit further, do your diagrams still make sense when printed in shades of grey? This determines whether your handouts are independently useful months after your talk, and it means time saved on adapting diagrams for publication.
Dark backgrounds? Light text on dark backgrounds looks gorgeous, but it doesn’t print so well. There’s usually an option to print in black and white, but look for it before you commit to a template. In my experience the default text usually converts well, but that stunning yellow you used for emphasis might get lost when everything else obediently prints as black.
Invest? A remote mouse/pointer is a good investment. Some of them can be set to warn you that time’s up by vibrating.
Presentation and/or handout? Presentations are nice because you can point to things on the screen and you can keep working on them till the last minute (which unfortunately just means more stress for some people). Oh, and they’re free and pretty, but we’re above all that, right? Handouts are nice because they help people to follow more complex material, provide a concrete reminder of ideas that people can cite later on, and reach out to people with schedule conflicts, who will often show up later in search of such goodies. The ideal is usually both, but see what applies to your situation.
Trim the handout? It might seem like a good idea to cut costs by printing only the important slides, but in practice it’s better if the handout contains the whole presentation, even contentless outline slides. Exact matching helps the audience to follow along during your presentation and to ask questions about specific slides. The alternative is to make the handout very obviously different from the presentation, but people will often wish you’d printed bits you never expected anyone to want.
4-to-1 printing (or 2-to-1, or 9-to-1). You get vast expanses of empty space when you try to print four slides to a page in PowerPoint, and most other programs don’t get it quite right either. Print from Foxit PDF reader to control exactly what percentage to shrink/expand to. (Strangely, in some versions you have to click Auto Rotate off and on before you can start manually rotating, and clockwise rotating works while anticlockwise doesn’t.) Incidentally, many programs print the slides vertically from right to left, rather like traditional Chinese. This can be fixed by changing enough page orientation settings from portrait to landscape.