Depending on the bit rate at which the MP3s were encoded, good ears can detect a difference in sound quality. For me, if the bit rate is 192 or higher then I am unlikely to notice the change.
In addition to what was said about quality, I'm not sure if Amazon uses any DRM in their MP3s but if they do, that MP3 will only be useful on the computer you downloaded on, and where ever else "they" allow you to use it. With the CD you can rip it till the CD explodes and put the MP3s anywhere you want. I seem to remember Amazon was going with DRM free MP3s. If so, then probably only the quality applies here.
Yes, Amazon does have DRM free MP3s, as does emusic.com (I think that's it).
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