I usually outline and arrange my presentations using Mind Manager from MindJet. That lets me get the ideas in order and collect the links, and also makes a fine online handout if you export it to HTML.
It can export into PowerPoint, as well, but since I usually use slides primarily for illustrations, with occasional quotes and video or audio clips, I normally create the slideshow from scratch. (I’ve heard good things about Apple’s Keynote, but I’m a Windows user, so I’ve never tried it.)
I do think it’s worth distinguishing writing the presentation from delivering the presentation. Presentation software is just an electronic version of the old-fashioned slide projector, and no one who used film slides ever wrote their presentation with a slide carousel. And it was a little more obvious, back then, that putting tons of text onto a slide was a bad idea. (It was also not easy to photograph the printout in order to turn it into a slide.)
Your presentation is not the same thing as your notes. The presentation is a live whole including your delivery, the audience, audio-visual aids, and also the text or notes you’re working from.
In many cases, a completely scripted presentation is dull—and doesn’t equip you for dealing with unexpected occurrences like total equipment failure or an audience that turns out to know either more or less than you’d anticipated. You should always be prepared to give your presentation without the computer, without the screen, without the speakers. The slide show is an aid; it can make things much easier and better for the audience. But the presentation is you and your knowledge.