I'm mostly writing this for students who need this information to turn in master-quality videos at the end of the semester, but maybe it'll be useful to others.
Ideally, you want to be working in a visually lossless codec all through your editing process. It'll take up more drive space, sure, but it'll perform so much better and you won't have to worry about double-compressing or stuff like that.
The big two at the time of this writing are Apple's ProRes and Avid's DNxHD. Both are good. They need to be installed on the system you're using to be able to use the codecs.
DNxHD is cross-platform, you can download it for free from Avid here, it's one of the many codecs included in the package.
ProRes is a bit better, but you can't encode with it on Windows. You can download it free from Apple here. However, if you don't have Final Cut Pro, Compressor, or Motion installed, it won't let you install it directly. To install ProRes codecs without those applications, you'll need to remove the codecs from the installer using a free application called unpkg.
When you unpackage the codecs, you'll need to move them by hand into the appropriate places on your hard drive. Luckily, they are mapped out for you. The folders you just unpackaged are in the directory structure /Library/Quicktime/ and /Library/Video/Professional Video Workflow Plug-Ins. All you need to do is move them into those folders at the root of your own hard drive, creating them if you don't already have them. Remember, you're putting them in the Library folder at the root of your drive, not the Library folder in your user directory. Obviously, you'll need administrator access to the machine.