Fuel in oil on Yanmar 3GM

Most likely your fuel pump or fuel rail is leaking oil into your crank case. It can also bypass the piston rings.
Either way you have a potentially dangerous situation as the engine can and eventually will run away on you. A run away engine will usually destroy itself in a spectacular fashion. Broken crank shafts, twisted connecting rods or pistons hanging out the side of the engine block are not uncommon.
Check you compression, if that's ok have your fuel system rebuilt. If your engine has a lot of hours on it you may want to consider an entire rebuild.

Thanks for the suggestions. When you say "fuel pump" do you mean the "lift pump"?

If it is the lift pump, what should I see if I take it off?

Thanks

Your lift pump will have a split diaphragm.

Appreciate the information.

If the lift pump is the problem, is it best to get a new one or can it be rebuilt? And any good source of parts in the Massachusetts area (and also recommendations for a rebuild)?

Some can be rebuilt, they have bolted together diaphragm housings. Others have pressed together diaphragm housings. The bolted ones have bolts around the diaphragm housing that are easily visible.
Myself I would buy a new one, but that's just me.
As far as a local parts supplier or engine rebuilder, I have no idea. Maybe someone a little closer to you will chime in.
Good luck, I would refrain from using you engine though.

Lift pump is a non-service item (even the screw together ones), Yanmar won't sell the diaphragm separately, you have to buy the whole pump. I went through this recently with my 1GM10, I replaced the lift pump, had the injection pump serviced (a seal leaked under pressure, it wasn't immediately apparent on their standard test, I asked them to test it again), had the injector cleaned, and replaced a whole bunch of other stuff while I was at it. And checked the compression, which was luckily fine. Seems to be OK now, mine was at the point it was trying to run away almost constantly, they are tough engines and no apparent harm done.

I have a related question: Should I drain my fuel tank from time to time and have the fuel analyzed as a routine maintenance item? I've never done it and I've been curious whether the engine is using fuel efficiently.

Hark...

Just pump some of it out from the bottom of the tank and leave it to stand in a wee clear bottle.
You can assess the condition of it from that.
Some owners leave a wee bit of mirror in the bottom of the tank and shine a flashlight in there from time to time to check the reflection, and assess the fuel clarity from that. The mirror must lie flat on the floor of the tank close to its lowest section.
It is worth a try.

Thank you very much, Rockter. I'll do that.

I have a 1985 3GMF.
That's not a real expensive pump.
This quote from a Blackstone oil test a number of years ago. "The only contaminant was fuel, and at 3.5% it's something to monitor. But fuel is a common find in marine engines, from trolling and idling, and hopefully this will improve on its own, without you having to do anything about it."
After this report I changed the pump. The next report had short hours on the oil, not much running at temp, and still excess fuel.
The summers where I have gotten good 2,3,4, 5 hour runs on the diesel, on longer cruises, gotten her up to temp & run full out for awhile, have had reports free of excess fuel.
Still, I think changing the pump is probably cheap insurance. Having something not fail during the precious little cruising time I get is worth $$.