Two tools I can mention, and I guess it's an answer to both questions (tools for presentations and tools for papers).
The first is Xfig, an ugly yet very powerful program for making figures, available for several platforms. I usually include $\LaTeX$ code and export as Combined PS/PDF/LaTeX, which allows me to compile with
pdflatex without having to change the input for the figures every time. Others may prefer to write code for their figures, but I've found that Xfig is powerful enough, and making figures is quite fast once you are used to the functionalities and the keyboard shortcuts.
The second is the book Trees, maps and theorems, by Jean-luc Doumont. It is not a tool to make or give a presentation, but to make or give a good one. I am all for simplicity when it comes to presentations. We all know, or understand, that a slide full of text might not be the best means of communicating a message or a series of messages, but this book goes beyond that kind of basic, "common sense" advice, giving guidelines on how to write comprehensible text in scientific papers (and slides), how to make figures that visually attractive and easy to understand, and even how to structure a document (you'd be surprised when you realize how "primitive" the intro-content-conclusions structure is). I could say more, but I guess it's better if you read some reviews out there.