I've pretty much figured out how to stay warm in the kayak even during these cold days. I typically start with a layer of UnderArmor (top and bottom) to wick away moisture, then a cotton t-shirt, then a thin layer of fleece (awesome stuff and totally essential) and then a windbreaker or rain top. I have a pair of neoprene kayak gloves purchased from LL Bean that are form fitting and keep my hands warm so long as I do not soak them. On my legs I will wear jeans or sweats (over the UnderArmor) and then a pair of booted chest waders. The only thing I haven't gotten right are the feet. I'm still looking for a really good pair of socks that I can wear with those waders.
Get a pair of the neoprene wading socks. I bought a pair last week at BPS and they make a huge difference. Simms wading socks, in the fly fishing section. $29.99. I wear them under my neoprene waders with 2 pair of wool socks
i place a car floor matt on the floor of the kayak to help keep my feet n legs warm and i also bring a black trashbag and cover my legs and lap(it absorbs heat from the sun and keeps legs from getting wet when im paddling) i also have a pair of fingerless gloves for when i'm fishing and fingererd gloves for paddling
Neoprene gloves are nice also for keeping the hands warm. Only pain is when unhooking a fish I have to take them off so I don't destroy them with the hooks!
I am new to this site but I have been kayak fishing for many years. I have to say you guys are breaking the #1 rule of kayaking, weather it be fishing or just paddling, especially in the winter. You need to dress for the water!! Unless you have been in the water when it is 40* or less, you really don't know what it is like. This time of year you need to be completely isolated from the water. Drysuit or at least waders and drytop.
Frogman is right, I use the waders but I need to order a good drytop. Gotta hope for the best but prepare for the worst, and it's short money if it does end up saving your life. That goes for you cartopper guys too. I've seen you guys go overboard more often than the yakers. Be safe.