I have observed (heard and then tested so as to confirm) the following “condition” as it relates to the widely debated issue of FLAC quality. The purpose of this topic is to gather opinions as to whether or not your observations are similar too – and therefore support – my own.

It is widely understood and accepted that a FLAC file while “compressed” is “lossless” as compared to its corresponding WAV file. Let’s assume (i.e. not debate) this is completely true. What I am noticing is that when the FLAC file is “played” via any FLAC player it sounds different from the sound of the “same” (equivalent decompressed FLAC) WAV file when played back via the same player that was used to play the FLAC file. This is specifically noticeable (to me) in the low frequency spectrum. The WAV has considerably more “sonic energy” that manifests itself as appearing to be a bit louder, wider in frequency range and perhaps even dynamic range as compared to the FLAC equivalent.

I’m curious as to your findings when you compare a FLAC file played natively as compared to the WAV equivalent played via the same player (for example, play both the FLAC and WAV via VLC media player) or practical equivalent, such as if the FLAC was burned to CD and you are comparing the FLAC played via VLC and the CD played via a CD player.

I am further assuming that the WAV file is a more accurate representation of the audio than the FLAC. This is to say that should you agree with the aforementioned, it would be preferable to play the WAV file or decompress the FLAC file before using it.

I am glad to read someone else has noticed this.  In thinking about it I concluded that there are still a lot of variables between the formats.  The codecs, cpu time, players, throughput.

I have settled on AIFF for now but I hope to learn more by reading other's experience and practices.

Thank you mapman and emailists. I concur with you Emailists, although I have not used AIF with a MAC. Perhaps to restate my point of this thread in different words, what I am saying is that it certainly appears as though it is "best" to pre-decompress the FLAC first - using say Traders Little Helper - and then once decompressed to WAV then play it. Perhaps FLAC players which decompress on-the-fly while playing does not do as good of a job as pre-decompressing. So mapman, while I agree that lossless is lossless, in my opinion (and emailists and perhaps others) while the file is lossless it may not be as good as when decompressed into its then uncompressed lossless state. 
It has to be converted to standard PCM format which is was format before it can be converted to analog.  So there is an extra step in the process.   If done properly it should not matter but may not be in some cases.  But the information content of the source is the same assuming the software that encodes the flac does its job correctly.  

So Flac may not sound as good in some cases or vice versa but if so its not because of the format.   Just like how different cartridges may sound better or worse playing the same record.  
Computer decompresses data, places it in the memory and adds timing to create and output S/Pdif (PCM). The only difference, assuming bit perfect conversion, can be jittery S/Pdif timing, that would add noise to music but dynamic range should be the same. Since computer timing errors would be very small noise would be added to mid and high frequencies. I cannot imagine how it could affect the bass.
Just as you assume flac is indeed lossless, I think it is fair to assume that the decompression algorithm on any reasonable player does its job correctly.

Have you tried zero compression flac? It is not compressed but has a flac header?

Systems that play from memory can decompress a flac file and then put the PCM into memory for playing. At that point, the computing to decompress is not important. Have you tried that approach?