SPCR rates the WD 5000KS very highly in terms of having low-noise characteristics. I looked up the drive on the wdc web-site and they say that the KS has a buffer-to-disk transfer rate of around 750Mb/s, where the AAKS rates around 930Mb/s (mega bits / sec). I think everything else is pretty darn equal.
I've seen a KS for about $111. The lowest AAKS I've seen is about $115 [newegg, go figure 8].
Get the AAKS if you can, but I don't think it matters too much. Hope that answers your question.
Of course, there's also the WD5000YS which is designed specifically for RAID configurations. Near as I can tell, the only real feature is the 1.2 million hours MTBF. There is about a $30 premium as well.