Undoubtly FLAC for storage
High-quality, also supports ID3 tagging quite well, while WAV or APE both sucks in tagging.
Hi Gellan and welcome, just curious as to why you would use ID3 tags for FLAC when Vorbis is that format's standard? From the xiph.org FLAC FAQ:
"FLAC has it's own native tagging system which is identical to that of Vorbis. They are called alternately "FLAC tags" and "Vorbis comments". It is the only tagging system required and guaranteed to be supported by FLAC implementations.
Out of convenience, the reference decoder knows how to skip ID3 tags so that they don't interfere with decoding. But you should not expect any tags beside FLAC tags to be supported in applications; some implementations may not even be able to decode a FLAC file with ID3 tags."