For my presentations I generally use S5, S5 Link. This “Simple Standards-Based Slide Show System” is web based and is capable of running on practically any machine. It both uses PHP and Java, nowadays these scripts will run on most hosting services. I am still working on my own S5 version. Although I already edited the layout somewhat I'm still not 100% happy with the looks.
The S5 slide show's are automatically generated by my site. I integrated the S5 system with the wikidoku installation by a plugin. This plug in can be found at: S5_Plugin