I generally write my presentations up in LaTeX and use beamer to convert them to PDFs for display. I don't really like PDFs though, they're big and unwieldy. I was just looking around at alternative methods and ran across the older Linux for Presentations Mini-HOWTO which lists a number of HTML-based presentation formats. This is definately the way to go, and with MathML (via itex2MML, see my mdwn itex post for details) I can generate most of the equations that I need to fit into a standard presentation.
The two grandaddy frameworks are S5 and Slidy. S5 goes back to 2004, and Slidy has been around since 2005, so they both go back a ways. The code you'll be writing is fairly similar in each of them, so just pick whichever you like best. If it matters to you, Slidy is a W3C recommendation
However, neither of these early projects seem to be actively developed. For example, this thread on the S5 Project Google group discusses fracturing in the S5 community. As people try to work around issues with the older frameworks, they've written up new frameworks. S6 wiki has some pointers to other options.
Personally, I'm going to go with S6, since the project uses Git for version control which is a Good Thing. There's also S9, which lets you build S6 presentations with some sort of wiki-syntax instead of HTML, if that's appealing to you. If you need MathML on Firefoxes before version 4 (which includes HTML 5 support), you'll need a framework like Slidy that supports XHTML.
Finally, there's a webslideshow Google group that tracks developments in this area.