I recently updated the nearly 2-year-old Rockbox build on my Clip+' to a current version to find not only noticeably improved battery life due to the frequency and voltage scaling patches having gone in (much appreciated since batteries aren't what they used to be), but the SD access related background noises are now significantly reduced as well. They are barely audible on my Soundmagic E10s and not in any way disturbing any more. Great! That used to be one of the bigger nuisances.
So what exactly did it? I went through the patches that have gone in, and aside from frequency / voltage scaling there were some SD-related fixes, so maybe those? Don't think it'll be the new USB driver, though that one appears to work very well - haven't seen it being recognized as a USB 1.1 device since.
(BTW, the scrobbler no longer makes things as sluggish as it used to (possibly the SD fixes?), database caching is back *yay*, plus you can finally listen to radio without having go into the menu (once the display is off anyway). The fancy USB HID feature was the first thing to be disabled though, as I have zero use for that on a tiny player dangling from a front USB on a PC under my desk.)
Anyway, you guys rock. (Lame puns go here.)