Kit bag(s)...ah the nightmare! The more kit the more bags and the more options for things that can go in them and what is best to take depending on what you want to shoot...hate it! lol
My CL L2 bag, which is the standard one that comes with the 200-400. Use that for my daily carry of the 200-400 VR with D3 attached.
It does close, honest!
Going to replace that soon as I believe ThinkTank have just released a bag that might be similar in size, but a tad larger.
My bag of choice for the 600 f4, a Lowepro Lens Trekker 600 MK II
Room for the 50mm in the front pouch.
My Lowepro Mini Trekker which I have had for years, since I had an F80 in fact before I went digital! I used that recently as my travel bag, it carried a D3, D300, 200-400 & my Bose QC2 headphones in the front pouch...a very good bag for flight travel!
Shown here with the 200-400, 50mm AFS & D3.
And as a 'short lens' bag, with my 70-200, 28-70 with room for the 50, 1.4x and also my flash.
And lastly (phew) my Lowepro Toploader 75 which I use for the 70-200 or 28-70 when I just want to 'go light'. Shown below with the 70-200 attached. I have a TL 65 as well but the D3 won't fit in that.