Audio Format Transcoding for Compatibility?

brandorf asks: "With the multitude of compressed audio formats that are available today, (MP3, Ogg, AAC, and FLAC to name very few) our music libraries start to spread across quite a few different formats. While this isn't a problem for desktop/media PC use, as programs like Winamp or iTunes have plugins available for almost every format. However, when it's time to start using a portable unit, it's unavoidable that some files will get transcoded. Have there been any studies or experiments as to how similar the codecs really are? Will transcoding from Format A to B sound worse than going from A to C? What's your experience with this?"