But most of us save audio files in digital format. Some use FLAC, I prefer wav as do all of the engineers I work with. There is a reason programs like ExactAudioCopy use wav as the default copying format.
For working with digital audio, you definitely want to work with wav. For long term storage of anything except original recording masters, I consider flac the better choice.
flac is a lossless compression format that allows you to use musical contents without decompressing the entire file. Unlike MP3., AAC, etc., the source material is not changed, but if you work with it directly, there can be artifacts introduced by the interaction of codecs and sound processing software. However, if your conversion software does its job correctly, you should be able to convert a flac file back to wav format and the results should bit compare to the original.
If I were doing sound engineering today, I'd probably keep multiple copies of original masters in the original (wav) format simply to avoid any potential problems, but I would compress at least one archival copy using software with some kind of parity recovery to guard against corruption. flac does not have any recovery capability, but for anything that is not going to be used as a master for further processing, it works just fine and saves a lot of storage.