X100 pouch needed
Another vote for the Black Rapid Snapr 20 - perfect fit around the x100 with the standard Fuji lens cap on, and comes with a brilliant, simple, integrated strap too. I use ot for exactly what you describe - it protects the camera while it sits in my backpack every day, and is easily accessible and usable as an over-the-shoulder case whenever I want. They also make a slightly wider model which is perfect for the x100 with the fancy lens hood fitted. I was so impressed I bought both.