Making use of backpacking-type gear, water filter vs. water, etc-space is still at a premium. I have some room for a secured item ahead of my footpegs but have been hesitant to put anything in the cockpit, from a rescue-recovery perspective. If properly secured and getting wet is not an issue, bag with drinks, soft cooler, etc. . . . do you place things there without hesitation for just your paddle to and front remote sites? (large freshwater lake could be like glass or up to three foot waves, heavy winds)
If you think about it, a kayak has over twice the volume of the typical backpack. So packing whatever you would take camping in a kayak should be no problem. I like your idea of keeping the cockpit free of clutter, although I've got room ahead of my foot pegs and behind the seat. Water in a water bladder (heavy) goes behind the seat. Something high volume and fluffy goes ahead of the footpegs (typically clothes or my sleeping bag in a compression drybag). Both are fixed and cannot move so entanglement isn't an issue. My secret: spend all your free time thinking about it. ;-)
Edit: you answered some of my questions in your post.
I also avoid at the feet I also avoid putting stuff at the feet. I am 6’ tall, so there isn’t a lot of space in front of my footpegs. I can fit a dry bag there, but I also know it is there (my fee touch). My 5’2" girlfriend has plenty of space, so we have placed bags in front of her feet. But this is something we only did when everything else is full.
Water bags do go well behind the seat. Good place for the weight (low and in the center of the boat).
Anything that goes in my cockpit has to be able to float, and also withstand water. So we leave a little bit of air in the waterbags.
Gear in the cockpit My wife and I both carry gear in front of the pegs on trips of more than 225 miles or 10 days. We pack very light and use much the same gear as backpacking; the issue is space for food. On longer trips we may start carrying more than is described below, but will shuffle things around as the food, carried in Ursacks, diminishes and provides room in the hatches. Typically, she will keep the fire pots and her dry-suit in front of the pegs, while I carry a bag of food and, if we are bringing one, the bear can. All of those are enclosed in either Outdoor Research or WxTex dry bags. I also have our 15 Liter tarp bag in my cockpit as a knee bag. Water is stored behind the seats along with a repair kit inside nalgene containers, bear spray, flares, etc. The gear in front of the pegs stays put for the most part. I’ve also carried a shotgun in the cockpit in high arctic waters to remind polar bears that I am not lunch. I’d rather have gear inside the cockpit than lashed to the deck. I have no concerns about exiting the kayak with my knee bag, much less the gear in front of the pegs. For a photograph of the gear that goes in my kayak see http://www.flickr.com/photos/umnak/page7/
I wouldn’t hesitate to stuff something in the space forward of your feet, as long as it was in a snug bag with no straps, etc. to possibly entangle your feet in the case of a wet exit.
Here’s a technical article I wrote about packing for kayak-camping:
The boat shown has two sealed bulkheads but is only 14.5’ long, and routinely carried all the gear listed, plus a bit more, including a gallon or two of drinking water. It may take several trips to work out your system of packing and your own gear list.
Although I typically prefer to keep a clear rear deck, in case of a re-entry, I have been known to carry items under the rear bungees if only paddling a few miles in good conditions. Say, to get out to an island where we’ll camp and unload some gear. But if conditions are poor when I launch, I will leave certain luxuries in the car in order to keep the deck clear.