in terms of offroading, having a manual allows me to control my speed more than an auto would. alot of times i'm so distracted with trying to manuever around and watch the terrain i realize i'm reving my gear slightly too high. if this had been an auto i would have simply continued to accelerate. and when you over-gas on rocky/gravel/slippery terrain, it could mean trouble.
and when i start a descent i just keep it in first gear and it keeps me at a slow speed without having to brake like an automatic would.