I'm surprised no one has mentioned MediaMonkey. I think it's a decent sounding player that has a lot of features and plugins and can play back files as high as 96kHz. As far as sound quality goes, well yes different encoders and decoders do have an effect on the sound because even though mp3, for instance, is a standard, there is no standard a developer needs to go by in creating his encoders and decoders as long as the file maintains the mp3 playback standard. Many hi end media players ( McIntosh, Meridian, Sooloos, etc ) will develop their own encoder / decoder for their players, as well company's like HD Tracks, etc. How much of a difference in sound do they make? I can say that it is a noticeable and easily percievable difference - at least on my gear. To me iTunes will distort and clip the tracks very easily ( no eq or plugins activated ). But MediaMonkey will give more freedom to the music before the distortion kicks in. The separation also seems a bit wider and deeper in MediaMonkey than in iTunes, but I guess this should come as no surprise given all the negative user comments floating all over the Internet about iTune's sound quality.
That said, I believe there is a difference, but can easily be masked by other things in one's system such as DAC's, how their PC is connected to their stereo, the capability of one's playback system, and of course, one's own hearing capability. Remember, even though all CD players must meet strict engineering designs in CD playback, we all know that CD players do sound different ( not just due to mechanical influences, but electronic too such as mentioned DAC's, error correction, software, etc ). MP3 encoders / decoders are no different.
Jimmy