[sassan]

If 300mm F/2.8 was an option, I would vote for it as it is one of the best lenses Canon ever made. Goes very well with TC 1.4x and also almost flawlessly with 2x to give you a 600mm at decent F5.6

With the two options you gave, 100-400mm is the winner without doubt. Problems or rather difficulties; as Christine said, It is an old lens and probably will be replace by Canon soon because of its blowing in and out while zooming and not being a whether sealed lens, it has the tendency to suck in dust. Not a good option especially with digital sensors, of course dust removal system of your 40D will take a good care of dust to great extend.