Change spark plugs. Check fuel filter for debris or clog. Fuel pump problem? Is it carburated or fuel injected? Could be a problem there. How about timing? These are areas where I'd start looking first.
Phoenix Arizona
~N.A.F.C.~B.A.S.S.~BoatU.S.~N.R.A.~A.M.A.~

If your motor pulls hard on a hole shot then loses power, check the fuel filter and flame arrestors first, then the rest of the fuel system. If it just generally lacks power start with the spark plugs and ignition system. That is the easy stuff. Not knowing the year or any specifics, it's hard to go past that, there could be a timing or ignition module problem or a loss of compression etc. Don't get to carried away throwing parts at it, it doesn't take long to blow a lot of money that way and make a trip to the marina worthwhile! Tom

I have a 1979 40hp merc. I have a problem when starting, the engine hits on one cylinder for up to 4 mim. before breaking loose and runs
perfect the rest of the day. I have replaced the plugs and used the merc. engine treatment , no help!
This engine runs as smooth as any one could ask other wise.

If your motor has individual coils for each cyl, check to make sure each cyl is getting spark. I have seen coils and ignition modules that will only work above or below a certain temp. If that is OK, check compression, you may have a weak cyl that gains compression as the engine warms. Tom

Ihad the same problem after boat had set for a while.The ethenal in the gas cause what looks like little brown BB's in the carbs. I cleaned the carbs out with a spray can of carb cleaner and drained the gas tank and filled with fresh gas. It mow runs great. Note you will have to take the Carbs off the engine and remove the bowles to clean. Hope this is some help.

Thanks for all help

engine runs good now
after new plugs and fuel filter and new gas on the tank

Joe