I use mine almost every day in the summer and I never empty it completely unless I suck it dry on a ride. Every once in a while ( like maybe once every two months maybe) I fill it with water and some bleach (or as snoop dog would say "bleeeee- atch") and let it sit overnight like Dave does.
It usually stays funk free.
Also, I typically fill it at least once a week with water from some back country source where I use aquamira (chlorine dioxide) poured directly into the bladder for treatment. not sure if that helps or not. probably not but it's what I do mainly so I don't get the runs.
I used to lei it dry out but found it got funkier that way. not sure why. *shrug*
My new method caters to my laziness.
Oh and also, I usually only put water in mine. On long rides any energy/electrolyte drink from gas stations gets dumped in, and on those I try to flush it out with water when I get back home then proceed as usual.