As with anything there is a cost/benefit ratio to adding an aftermarket system to our X5's. I don't think it will affect value much to most buyers, negatively or positively. Done right though and it will be a definitely selling point to some buyers. Of course done wrong and it will be a detractor.
My cost/benefit is always based on the enjoyment factor. Up front though, I'm an audiophile so I value tunability and sound quality. For this reason I've always thought doing an aftermarket system (head unit, amps, etc) was a worth while investment in my vehicles. I can't wait to do a full setup on my 4.8is like I did on the 4.4i. I will be gutting the entire vehicle... maybe even pull the dash out so I can have it leather wrapped. To each their own right.