Let's start with rods and reels. I like to back off on the reel's drag for the winter months of inactivity. Loosen it up quite a bit. I've been told that this makes the internal components of the reel happier. If you're a do-it-yourselfer, some lubrication in the reel is a good thing every now and then. If you don't feel comfortable taking a reel apart, take it to a reel repair shop and have them do what should be done. They'll be able to provide you with ideas on needed maintenance.
I like to take about forty yards of line off my reels in the fall. I don't add new line until spring. By doing so, I know that I'm starting the season with fresh line. If I don't take the line off now, I will be tempted to start next season with old line, and that's a bad idea. I rarely take all the line off my reels. I just strip off about forty yards, then tie new line to the old line remaining on the reel.
Open up your tackleboxes and take an inventory. Try to remember what lures you lost during the year and make a list of lures that need to be replaced. Check hooks for rust. Leave the tacklebox open for a few days to allow it to dry out. While you're in the tacklebox, organize it. I like to keep eighth ounce jigs in one area, quarter ounce jigs somewhere else. Same thing with crankbaits. Segregate them by size. It's much easier to find what you're looking for when stuff is organized.
Now let's move out to the yaks. If you have any electronics make sure the batteries are charged before storing them. Lots of kayakers take their batteries out of the boat for the winter, others just disconnect the wires. I leave them in the my kayak and have had no problems.
If you have a trailer check it for working turn signals and brake lights. If there is a problem, get it fixed now. If you don't, chances are you'll still have the problem next spring when you want to go fishing.
I like to take the depth-finders and other electronics off the kayak and keep them in the house during the winter. Go through the kayak's storage compartments and clean out the stuff that doesn't belong there.
And, when you get all that done, get the ice-fishing gear out and start preparing it for ice-fishing. If things work out, we'll be out on the ice in just a few weeks, and we want to be ready when the ice is safe for fishing.