Don't know if this will help others, but thought it might be a neat thread to start.
There is a lot that has to be done (assuming that the dealer (or the owner) does everything by the book). Obviously you should have the service manual (get it at SIM Yamaha (from this forum) Part # LIT-18616-03-13
Some of the items on the check list are no-brainers. I'm going to list them in two different sections. "Passive Maint." (looking over and making sure things are within spec) and "Active Maint." (where you actually have to "do" something).
Battery (Electrolyte Level, Terminal): Check/Charge/Replace ::: PASSIVE.
Simply look at the battery, check it for corrosion, check the fluid level, and check the voltage. Make sure it is within the proper voltage range.
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Cooling water leakage: Check/Replace ::: PASSIVE.
Simple enough, look around the motor (have the hose connected to the flusher (not the ears, but the built-in flusher) and look for leaks coming from places it shouldn't.
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Engine starting condition/noises: Check ::: PASSIVE.
Start the motor, how does the starter sound? If you hear something that doesn't sound right. Check into it.
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Engine idle speed/noise: Check ::: PASSIVE.
Should be steady and around 600 RPM.
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Engine Oil: Replace ::: ACTIVE.
You actually have to change the oil. This means follow the procedure in the manual for changing the oil. There is also a great link in the SIM (that takes you to another site) Yamaha forum for this. It looks very easy to do. Just follow the directions and take your time.
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Engine Start Switch/Engine Shut-off Switch: Check/Replace ::: PASSIVE
This is as simple as making sure the key and the lanyard switch works. Test it. Done.
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Fuel Filter (can be disassembled): Check/Replace ::: ACTIVE.
Page 6-9 tells all. You'll need a MityVac like this:
If you want to do it right. For some reason, I can't see a dealer doing all of this, but maybe somebody here can correct me.
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Fuel Hoses (High and Low Pressure): Check/Replace ::: PASSIVE.
Look at all fuel lines when running. If you see any leaks. Replace. Look for rotted or messed up ends (where they clamp), etc.
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Fuel/Oil Leakage: Check ::: PASSIVE/ACTIVE.
Sort of part of the previous check. However if you look at page 10-13, it is a little more detailed. Basically (it seems to me) a deeper "check".
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Gear Oil: Replace ::: ACTIVE.
Follow the instructions on page 10-14 and 10-15. If you can read, pretty easy. You'll need the proper pump to pump the gear oil in from the drain hole and make sure no air bubbles. Just read - not too hard sounding.
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Greasing Points: Grease ::: ACTIVE
This is where the manual REALLY saves your ass. There are a number of points that require different types of lubricants. Page 10-15 and 10-16 are golden here.
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PTT Unit: Check/Replace ::: ACTIVE.
Another one of those things that I just don't see the dealer doing. First, Just checking the PTT Operation is easy. Does it work? Does it sound right? If so -- you're good. Checking the fluid is another story (Page 9-33). I'll ask others to chime in about this that are either in the know or have done it themselves...
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Propeller/properller nut/cotter pin: Check/Replace ::: ACTIVE.
First off, you have to do this to get tot eh fitting behind the prop to grease it (see "Greasing points" above. Second, I think it is worth it so you don't have to fight the prop later on in life. :D
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Pilot Water: Check ::: ????????? I have no idea, since I can't find "pilot" anywhere on page 10-11 as per the reference page. I have to think it just check that you have "pee stream" -- but I don't know.
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Water Inlet: Check ::: PASSIVE.
Pull the screens and look around for growth or blockage.
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Wiring harness connection/wiring coupler connection: Check/replace ::: PASSIVE.
If something doesn't look "snapped" properly investigate. All couplers should be properly "seated".
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Yamaha meter/guage: Check ::: PASSIVE.
See if everything is working with Command Link, etc. Read the Comman Link manual for more informaion.
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There you have it. Might be kinda interesting to see how many of these things people are familiar with and their thoughts of procedures, etc.
Take it easy,
Pete
F250B Yamaha Initial Service (20 Hour) in the Tech Manual... 
