So which file format is best for saving your slides? It depends on the situation, but it's almost never the default .pptx you're offered. I made a little graphic below to act as a decision tree for choosing how to save your PowerPoint - click on it to be taken to a larger CC-BY-SA version on Flickr.
What it comes down to is this. Saving your slides as a .ppsx file - a PowerPoint Show - is usually the best option, because it opens the PPT up in Presentation View right away. This looks SO much more professional than the default .pptx PowerPoint file, which opens in edit view, revealing your notes if you have them, and the first few slides. Your audience seeing behind the curtain in this way isn't the end of the world, but why do anything to reduce the impact of the presentation you spent ages creating?
A .ppsx file will keep any animations you have in your slides (and embedded video and audio) and unlike a PDF it won't compress your images, so they'll remain high quality.
However, sometimes you need to use a PDF - mainly when you've used non-standard fonts. PowerPoint claims to be able to embed fonts that aren't included in the Office Suite (but which you download yourself) so they'll work on other PCs - I've found this to be lies, lies, and more lies... It simply won't work - either for presenting on another PC, or for uploading to Slideshare. So saving as a PDF sorts this out - it retains your exciting font choices, and keeps things the right size and shape (you may have to go into the Save Options and untick the ISO box if your PDF doesn't behave itself the first time you save it - for example if Transparency effects aren't correctly rendered).
I also use PDF if the PC I'm presenting on has a different version of PowerPoint to the one I made the slides on - or if I don't know ahead of time whether it will. The version of PowerPoint shouldn't matter but it does, and the other day I had to subtly reformat a whole slide-deck after checking it on the latest version of Office and finding it had mucked around with the font-size for no good reason.
PDFs are the safe option. They work on pretty much ANYTHING. Lots of people never present with PDFs because it simply never occurs to them, but trust me it works fine! I do it 99% of the time because 99% of the time I use non-standard fonts - just click View then Fullscreen Mode and it works exactly like a PowerPoint in Presentation View (including using a clicker to move the slides along).
(There have been a couple of occasions where I've forgotten to do this, and turned up with a regular PowerPoint file to present on a machine with none of my special fonts installed. This has resulted in frantic downloading and rediting and saving in a panic, and is not recommended...)
NB: Never ONLY save your slides as PDF or PowerPoint Show - you need the .pptx file to actually come back and edit them later.
So next time you're saving your file, check if you really need to use .pptx, or whether another format is more appropriate.