Media Center is, of course, the reason this whole site exists. While not open-source itself, it is the best media manager that I have used. Not only does it rip, burn, organize, and tag multiple formats of audio, but also organizes images, movies, and other documents as well.
Flac is a lossless audio codec. I use flac extensively in my own collection (which is why I started developing the plugins), and it is supported by a plethora of open-source software and hardware.
The Wavpack format site. Wavpack is a hybrid lossless or lossy coded. It is open-source and is fairly widely used.
Oblong wrote the first flac plugin (decoder only) for MC. Unfortunately he hasn't been able to keep it up to date. It also seems like it might be gone anymore (2007/04/21).