Re: 2006 Mercury 50 HP Won't start!
Rule out the simplest things first...
The motor may have flooded. Try to start it after letting it sit for a day. If it still does not start, then it likely was not flooded because after a day of sitting, the excess fuel would have evaporated/drained out.
Make sure the throttle is in neutral. It sounds dumb, but sometimes it looks like it's in neutral but isn't completely clicked in. The motor will not start unless in neutral, although if your motor is trying to start and not catching, this probably isn't the problem.
Make sure the lanyard is in. The motor will not start with it out. Same as with being in neutral, this probably isn't the problem because it sounds like your starter motor is engaging and trying to start the motor. Still, just rule it out before going any further. We try to troubleshoot from the least costly to the most costly things.
When you say it tries to start, that suggests that the battery is turning the starter motor. Perhaps it isn't turning it fast enough to get the motor going on its own. This could happen from a low battery, perhaps from leaving equipment on (fishfinder, radio, lights, etc) while out on the water. You could try to start it on another battery (even a car battery) or fully charge the boat battery. Also check that the battery terminals are clean and the wires are tightened down on them and making good, clean contact.
If these initial checks have failed to start the motor, then look at fuel. When you said you may have run out of fuel but then ruled it out, you may not have ruled it out yet. You may have run out of fuel and when you refueled, you may not have primed the primer bulb enough to fill the fuel/water separator, fuel lines, fuel filter and carb bowls. You have to pump the bulb until it's hard. Otherwise, you will not be getting fuel all the way to the carb bowls, where the motor actually draws its fuel from.
If priming the bulb until it's hard fails to help start the motor, then look at spark. Remove the spark plugs. Replace the rubber cap on the plugs and hold the threaded part of them onto the engine block to ground them. Do this one at a time and don't actually hold it with your fingers or you could get a shock. Turn the key while the plug is grounded against the engine block and look for a spark in the gap of the plug. You will not see it in the sun. Do this at nightfall. You should have a bright blue, strong spark in each plug. If you don't, clean the plugs and try again. If the plugs were dirty (fouled), look for a photo online of plugs that look similar and you'll have an idea of why they were fouled.
If you don't have spark in one or more plugs, then start reading up on the ignition system. If you do have spark and you've tried everything up to this point with no success, post those results. You will have to start troubleshooting the less likely, and more costly possible problems.