- Make the text on your title slide good and big. That way people will be able to read it more clearly on when it's shown as a thumbnail on your homepage and elsewhere.
- Slideshare proclaims to upload your speaker notes with your slides. In my experience, this only works for .pptx files (i.e. 2007 and later versions of Powerpoint), and only the first time you upload. If you make changes and upload your presentation again, the notes won't be updated, and if you've added extra slides your notes will end up out of alignment.
- Slideshare doesn't reproduced animation effects in your presentations, so if you have one slide on which various things appear one-by-one, they'll be there together in one go on Slideshare. I get round this by making individual slides for each new appearing thing.
- EDITED 23/11/11. Lastly, Slideshare only has a fairly limited repertoire of fonts that it supports automatically. Embedding your fonts in a presentation seems to get round this OK if you save your file as a .pptx file (that's the newer version of Powerpoint, from 2007 onwards). Normally I'd recommend that you save your files as .ppt, as the newer .pptx format cannot be read by people who have the older software (or who are running open source software), but for the purposes of Slideshare it seems that .pptx is the way to go (see also speaker notes, above). If you don't have access to newer Powerpoint, your best bet is to check in advance whether your fonts will work: here are some slides that show a few fonts that do and don't work out of the box, or try uploading a test slide when you're planning your slides.
- EDITED 23/11/11 I forget to say in the original post that you should never put important, or clickable (yes - add clickable links in your Slideshare slides, that's where they're useful, not in the slides you show in person) links near the edge of your slides. You never know what will be cut off if the projection is bad, and clicking at the edge of slides on Slideshare makes them advance or go backwards. So links near the edges are no use.
As for Prezi, well, I made a quick Prezi about that: