Interesting thoughts. I think you've got the three categories right, although depending on the time of year, I might move warm clothing from "as dry as possible" to "MUST be dry." Also, since my food is stored in Ziploc bags, it (along with the stove, etc.) could drift into the "definitely wet" category. But those are both minor, personal distinctions. Your basic point remains: how do you keep the wet stuff from "contaminating" the stuff that has to stay dry?

I've found two answers: stuff sacks and extra pack pockets.

Stuff sacks are mostly waterproof (yes, there's that big hole in one end - but that's not a big problem if the water isn't running off the stuff inside.) So, anything that needs to stay dry, or that is wet and needs to be segregated, goes into a stuff sack. If it's truly critical (sleeping bag, for example), it goes in a "dry sack" which is simply a seam-sealed, roll-top stuff sack designed to provide a waterproof seal.

In my own case, the sleeping bag would get a dry sack; clothing would go in a plain stuff sack, as does food. (Clothing and food might both go into Ziploc bags before going into the stuff sack, if I knew I was in for several days of rain.) My tent goes into two stuff sacks: one for the fly and ground cloth (if I'm using one); one for the inner tent. That way, the soaking wet fly won't wet the relatively dry inner tent.

The other option is to either buy a pack with lots of exterior pockets, or use add-on exterior pockets. You keep the wet stuff outside the pack. My own favorite example of this type of pack is the Osprey Kestrel 48. It has a decent "shove-it" pocket where some wet things can ride. It also has a two-compartment lid pocket, so one pocket could be designated for small wet items (gloves, or maybe a rain hat?) It also has two long, vertical zippered exterior pockets. Typically, I'd keep rain pants in one and rain jacket in the other; however, in prolonged rain, I'd move the tent to the outer pockets (fly in one, body in the other), since I'd be wearing the rain gear almost all the time. When I wasn't wearing it, the rain gear would go in the "shove it" pocket.

The two small side pockets are used for things that will be wet regardless of weather: my water bottle in one, and the filter in the other.

As far as a "waterproof" pack bag - there really isn't any such thing. They are all highly water resistant (I've never had rain soak through into one), but they aren't absolutely waterproof. That's why we have pack covers.

Which brings us to another alternative for separating wet from dry gear: pack liners. Essentially, a pack liner is a giant "dry" stuff sack/pack cover that goes inside the pack. You put everything that you don't want to get wet inside the pack liner, then close it like a dry bag. Then you put the wet stuff on top of it (or around it or under it, depending on your own preference.) The wet stuff is segregated from the dry stuff, and it doesn't matter if the pack itself is wet or dry inside. I've used one, once, in heavy rain, and it worked pretty well. My personal preference is several stuff sacks, but that is strictly personal preference for subjective, not objective, reasons.