Add fuel stabilizer to the gas tank. Use a fuel stabilizer that is designed for ethanol blended fuels.
Warm up the engine to operating temp & change the oil and filter. You can use a fluid extractor or drill pump to expedite the process. Replace with amount specified by the engine manufacturer (some of this will be poured directly into the filter before installing it). Engines with flat tappet cams, i.e., Fords & possibly some pre Vortec Chevys, should use an oil containing the zinc additive ZDDP such as Valvoline VR-1 Racing Formula 20W50.
Warm up again if necessary & change Transmission fluid. Keep track of how much comes out & replace it with the same amount of Dexron/Mercon (your transmission may require something different depending on your manufacturer).
Warm boat back up to operating temperature, lift the flame arrestor up & fog throat of carb/throttle body intake until it smokes or the engine dies (approximately 10 seconds or 1/3 can). Kill the engine. Do not fog dry intakes such as the PCM GT-40.
If you are going to add antifreeze, drain the block first; RV antifreeze should not be diluted. Then, reinstall the drain plugs. You can add antifreeze in a couple of ways. You can add 5 gallons of Pink RV Antifreeze or Sierra (propylene glycol) to a bucket & suck it up with the intake hose; fogging as it runs out. Alternatively, you can add antifreeze by pouring the antifreeze into the hose leading to the thermostat housing through a funnel. Roughly 3 gallons of antifreeze is required if you do it this way. With PCM marinizations, there is a bypass that will allow the antifreeze to get to the block even if the engine is not warm. With other marinizations, warming up the engine is advisable if you use the "pour in" method. Note: RV Antifreeze may not be recommended for boats with Aluminum heads.
If you have a metal flame arrestor, spray the flame arrestor from the inside out with carburetor cleaner. Dry thoroughly before you reinstall it.
If you don't add antifreeze, pull the two plugs on either side of the engine block & remove the plugs on the back of the exhaust manifolds. On PCM engines, there is another plug in the piece connecting the hoses coming from the thermostat housing & going to the engine block. If fuel injected, removing the starboard side block plug may involve removing the knock sensor. Use a coat hanger wire to make sure the openings are free of rust particles & debris. Wrap the plug threads with Teflon tape so they won't be hard to remove in the future (you'll be excited in the spring & won't want to do this). Put plugs (including bilge drain plug) in a plastic bag & zip tie it to the steering wheel so you won't forget to reinstall the plugs come spring.
If you haven't added antifreeze, disconnect the raw water hoses at their low points and shake them a bit. Blow through them if necessary. Remove the hoses from both sides of the transmission cooler. Make sure the transmission cooler doesn't have debris in its screen. Leave the hoses disconnected. Remove cap & screen from raw water strainer & make sure it doesn't have any water sitting in it.
Remove engine kill switch & spin the engine over for a few seconds to remove excess water in the pump bodies. Reinstall the kill switch so you don't lose it.
Remove impeller if you don't plan to replace it in the spring. Keep this impeller in the glove box as a spare if you need one.
If you have pitot style speedometer pickups, with a needle, check the pickups to be sure they are not blocked. Next, remove the speedo lines at the front of the boat & blow the water out of the lines and ballasts. Reconnect them when you're done.