I mix it up. I spend the first ten minutes or so in a low gear, spinning with little resistance, just to warm up the knees. Then I spend the next 20-50 minutes working a varied program of high resistance/low resistance, to try and keep things interesting.
Usually it is easier to set the trainer to a moderate resistance and use all of the different gear ratios that you have on your bike to change the total resitance. You can do this quickly and is a better simulation of what it is like on the open road.