I count them. Anything over ~17mph on my trainer is actually more difficult than it is on the road. After a few weeks on the trainer my first ride outdoors feels really easy. Plus, in the dead of winter with ice/snow on the roads it can be a lot more fun to think of hopping on the trainer to do 25 miles than to think of doing 90 minutes.
My log always shows whether the miles were on the trainer or not, but my total for the week is my total.