As for MP3s, they are a loss format. That means during the conversion to MP3, your converter will drop out some frequencies. MP3s will actually drop out frequencies that are audible to the ear, which is why lower bit rate ones sounds the way they do. Some people will only encode their MP3s at a high bitrate to get a near CD quality file- however at that point you really defeat the purpose of making an MP3 because the file size is much larger. The standard MP3 bitrate is 128k which isn't bad. The average listener probably can't tell the difference between it and the original CD, but I can.
There was some big stereo convention where the owner of a company that makes super expensive speakers played some music on his speakers and asked the people there to guess what source he used. They said stuff like "oh, it must be one of those top of the line CD players with features x, y, and z and it must have blah blah blah." I turned out to be and ipod. I don't know what format he was using on the ipod, but still, it shows that expectations can color what we here. As far as the stuff about vinyl being "warmer" goes, it might not true. People may just think it sounds warmer because they go in with that expectation.