Press F1 to enable them. You will have to press F1 every time you load a save.

Press F8 now. Version 1.0 is here, and now F1 is the help menu.
1-Heal everything(Crew/Hunger/Morale/Health)
2-Teleport all friendlies to ship
SHIFT and 2- Spawn loot chest
3- Cannonball to mouse
SHIFT and 3 at the same time- Kill all enemies
4-Teleport captain
5-Random weapons/items and lots of gold
6-level up all
7-Crap
8-Clean poop(WARNING:causes insanely glitchy sound if you press this and there is no poop left. It makes you pick up a corpse, and then your ears get destroyed.) Doesn't work anymore
9-Three extra crewmembers (WARNING: Can cause lag if you spam this to get tons of crewmembers. They all start talking at once, and it lags.)
SHIFT and 9- Animals

Its a violation of common sense. You have to drown your captain but not quite, and quickly use cheats to recover him(or make sure he has a life buoy item, or the swimming skill).
You can't just momentarily dip in the water, you have to stay in there and go deeper untill the eardrum-breaking noise stops.

The commenters for informing me of new cheats. I haven't played Pixel Piracy since 1.0, but I still maintain the guide.

The Devs disabled/removed cheats on this day. This guide is useless until cheats come back.

Cheats are apparently back now(2/19/2016)! Old cheats still work, but you cannot Clean Poop anymore.