I usually have anywhere from 5-10 MM worth depending on the bike. You should consider handlebar positioning, something that would be comfortable yet will work for climbing and descending. Also, if you plan on selling the fork later it may be better to keep a little extra tube left say another 5-10mm where the stem clamps. You would need to put spacers on top also if you do this.
Personally I leave extra tube at the top and put a spacer on top. That affords alittle leeway in terms of positioning the stem up or down. Hope this wasn't too confusing.