I have a 600mm, and I use the LowePro LensTrekker 600 AW backpack. I carry and keep the lens in this pack - hood reversed, no leather cover. The small external pouch can hold a set of Extenders, a polarizing filter, and the hood for my 16-35 which is kept in a LowePro lens pouch, hook/looped on the outside.
Carrying comfort is good, I wish they had a larger pouch as I am not real fond of stringing lenses on the perimeter of this bag, too easy to bang them into things...