I like the PDF versions because I can load them in my iPhone. The manual is always with me then. Other than that, paper is better.
My usual mode of operation:
1. After buying a new product, read each page of the manual reverently, enjoying and savouring each word and diagram. After reading from cover to cover, place it carefully back in the box.
2. From that point on, hit google if I need any answers - cant be bothered getting the manual out again.
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Most of the manuals to my camera gear is still in the original plastic bag.
The link is the one direct from the camera's CD which I saved to favourites.
That was my complaint really.
As me eyes are a bit challenged for close work, I like both!