I have taken mine through an automatic carwash. The only problem I had the last time I did it, they had installed blowers and it really does rock the car a bit. Not sure I would choose the option that had the blowers drying the car. Otherwise it did fine.
Some owners have problems with the traction battery getting too low while using AC in hot weather. For best results, either don't use AC very long, or make sure the traction battery is well charged before you must shift into Neutral. This is discussed in numerous threads in the regular GenIII forums. If you have a standard QWERTY keyboard, check which letters are adjacent to 'o'
Some have complained that the roof has partially collapsed/pushed in. Some have said it was a permanent dent, some said they heard the roof give and pop back out. But, these claims were in regards to the PriusC.
The automatic car washes with the automatic dryers always lift my windshield wipers up. I've only used them twice and have not returned since then.
Just make sure your battery is pretty well charged since you put the car in Neutral when going through the wash and the battery does not charge in N.