Fred Kaplan is apparently writing for Slate now*, and he correctly points out that digital music often sounds terrible, either due to poor sampling or poor encoding. He recommends using an outboard DAC to correct the problem. It's a great suggestion for people who listen to music in one spot using high end speakers or headphones, but not at all practical for those who are mobile, using an MP3 player or a smartphone as their playback source. Aside from echoing his related note to bump up the encoding rate when you rip music or download higher quality encoded music in the first place, the best suggestion I can make for mobile music listening is to invest in higher quality headphones. My first pair of Shure e535's had an almost magical ability to smooth out ragged MP3s without losing any detail (as well they should for $499). When they broke on me, Shure shipped out a replacement pair, but the new model doesn't sound quite as exceptional to my ears in the MP3-magic area -- it is still a fantastically neutral pair of headphones with exceptionally clean mids and rich bass, but jagged highs due to MP3 encoding faults still sound jagged on my new pair. The drivers are supposed to be identical, so I'm not sure if I got lucky on the first pair or less lucky on the second (or that I am/was hearing things that weren't there. Also a possibility).
I love the Shures, but my headphones of choice these days are etymotic's flagship ER-4's, which are hardly new, but have been transformed by custom earpieces etymotic had made for me. The program, which I called out in my Holiday Gift Guide, is called CUSTOM•FIT, and costs $100 (in addition to the cost of headphones). If you care about comfort and noise isolation, it is worth every penny.
*UPDATE: Fred got in touch to point out that defense and foreign policy are actually his primary coverage areas - and he modestly left out the part where he won a Pulitzer on those subjects. I know him from his sideline as an A/V writer.