When I'm packrafting, I usually opt for a shoe that drains well above all else (like the Salomon Tech Amphib). If I'm trekking any meaningful distances, then I just wear the shoe that I like to trek in.
As the temperatures drop, I move to a Gore-Tex shoe (I'm currently using the Inov-8 GTX 288), which helps trap warmth. It also traps water, so I get pretty serious about applying a skin protectant (Hydropel, Bodyglide, etc.).
In the packraft, I wear a pair of midweight wool socks under a 5mm neoprene sock (thick!). If temps are cold (less than, say, 25), then a VB sock between the wool sock and the neoprene sock does help.
On the trail, I walk in this squishy setup until my feet get sort of warm, then switch to a thick wool sock and a goretex sock in the goretex boot, and stow the neoprene socks and wet socks (I put these in a gallon ziplock and sleep with them at night so they don't freeze). This setup seems too hot for any temps higher than freezing, but seems OK below freezing.
For hands, I use a Goretex over mitt on top of a fleece glove on the water and trail, and I carry a spare set of fleece gloves or mittens.
Oh, and dedicated sleep socks (I use thick R3-style fleece) are a nice luxury.
Mornings are the worst, of course, especially if you are getting into the boat right away.
A fire every night helps take some of the edge off.