I have a Tamrac Superlight 48 that I used to use for my F3 and winder (but is now holding my Mamiya TLR). It is very deep, but may not have as much padding as you would like. Not sure that they make this model any more, but similar models should also work.
Many of the Domkes can handle the F3/MD4 with no problem. Domke F2 can fit 2 bodies/motors with 4-5 lenses, flash and a lot of film; the F6 is a bit smaller - maybe 1 F3/MD4 plus FE or FM body and 3-4 smaller lenses. They don't have much padding except on the bottom, but the canvas is heavy and they tend to mold to the shape of your hip over time. I've never cared for the metal clasps on the flap, but they are very secure when latched and make it difficult for someone to easily reach into your bag on a crowded sidewalk.
I usually have my F3 with MD4, and several lenses, in a Domke F3x that has many thousands of miles on it. It's a great bag. Sometimes I use a Domke 803 satchel with inserts, but that means taking the lens off to stow the camera.
Another vote for the Domke F2. I carry (typically) an F6 (or F5) and an F3HP/MD4-MK1 (or an F2AS/MD2) and four or five lenses in mine (along with a couple of rolls of film and, on occasion, a selection of filters). These bags are well- padded and well-constructed (mine is a decade-and-a-half old and still looks pretty good...all things considered). Of course, on the other hand, if you have too much disposable income, you could always check into a Billingham ( the equivalent to the F2 - size-wise - will run you around $500 and change, with shipping).