You should check out SecurityInABox.org. It's a complete guide to protecting your computer and securing your communications using off-the-shelf software that's designed for people like human rights advocates who work in countries where their efforts may not be appreciated by the government. Of particular interest is Chapter 7 (How to Keep Your Internet Communication Private) and Chapter 8 (How To Remain Anonymous and Bypass Censorship on the Internet). Some of the information doesn't reflect recent developments--I'd assume that Skype is less secure than everyone has previously assumed now. More on PRISM shortly.