I already have packs for mountain biking, overnight hikes, day packs, messenger bag... So I just use a top-loading case for my 645NII with lens attached (something like
this although mine is a different brand) and then just pack it into whatever pack I am using. If I bring any spare lenses or other kit they come in their own cases. Keep things modular.
Tripods are a pain, I fasten them to the outside of the pack somehow but they tend to get banged up, especially when I am mountain biking. A lot of times I just bring my heavy duty gorillapod.