If you ignore sound quality or if you like bassy sound or if you use the supplied Apple earpods, version 1.0.4 is the best.
Otherwise use version 1.0.3, which fixed the "whine" and in my opinion also gives the best sound quality when used with good headphones. But 1.0.3 also has other drawbacks. You cannot play low-bitrate or mono MP3s. Menu response is also much slower/jumpy.
Some people still prefer 1.0.2 because it has a little less whine than 1.0.4 while still giving a very bassy (too muddy in my opinion) sound.
Since I don't use any mono or low-quality MP3s and since I don't use the Apple earbuds and I also like crisp highs and clean, undistorted bass, I use 1.0.3.
YMMV!