What im seeing here is people seem to be in agreement, just go for the gold like ive been doing. A couple of suggestions other than that came up, such as picking up black animals, picking up every snake, and getting gunpowder from empty forts.
Some of these suggestions are for gold, but gold is irrelevant on this topic. You'll get more than enough just turning in the gold animals, what you want to focus on for the Merchant Alliance is rep, and all the not gold animals are worth the same rep, next to nothing. Same goes for if you happen to find a banana or cannonball crate, friggin worthless. I even turned one in for a message in a bottle quest, still worthless. Maybe it would be worth more if it actually came from a voyage.
Gunpowder barrels are the only exception. Off voyage, worthless. But as part of a voyage, their rep gain is small, about the same as a non gold animal for a voyage, so my rule of thumb is to only bother with them if a) i already have them and there is also a gold animal on this voyage or b) if the voyage asks for 3 or more. Since they are so easy to find and get, 3 will make you about as much as a gold animal and wont take hardly any time. But if its less than 3, i don't even bother sailing to the fort to grab them.
Also i thought this was a given but, NEVER sell ANYTHING that isn't part of a voyage. EVER. The rep gains for it are worthless. Don't worry about gold, gold is everywhere you will get gold naturally just focus on rep. Currently im 27 and it seems like it takes 8 gold animals from voyages per level, which is already a b**** and a half, i shudder to think of what is required for 30+