I've tried the HPG snubby kit bag and currently own their waistpack. I never got comfortable running with the chest bag, not just for the gun factor. While I think that most folks won't notice, some will. I have friends that use them who have gotten off-hand comments from strangers when running in urban environments. It might only be one percent of one percent of the criminals who notice such things, but isn't that the ones we really need to worry about?
For me it comes down to wanting to look like every other runner you see either in the woods or on a city greenway trail. I'm willing to give up some comfort to do that. That has payed off a lot with the ability to go for a run and then transition into a social situation without changing anything about my set up.
Besides the belt and holster setup mentioned earlier, I like wearing shorts with multiple pockets like the Brooks Sherpas. It lets me spread junk around and the wide waistband keeps stuff from bouncing around. Paired with a handheld bottle/BeFree filter and on the rare occasion a minimalist vest.