So, I'm a big fan of the Port Royale series, and I'm wondering if there are any similar games out there. Games with RPG elements like Ogre Battle and OB64 would be great. M&B Warbands is nice, but it's single party, and trading and economics don't really matter at all.

I'm always looking for games like this, but they don't really seem to be out there.

Well, the Patrician games are like a sibling series (with some increased difficulty) to Port Royale, so you should give that (I recommend Patrician 3) a shot. However, that doesn't have RPG elements.

I bought (but have not yet played) Port Royale, but it seems very similar to the Space Rangers series, which takes sandbox trading/combat and puts it in a sci fi outer space setting, including and rpg system. Space rangers also has optional rts, text game, and arcade game content on top of that. Might be worth your time to check out.

While the Space Ranger games are great, they are actually quite different from the Port Royales. While the formers are wide-open sandbox games with a wide variety of activities to pursue in order to get money, advancement and recognition, the latters are economic games with some additional gameplay elements.
That said, if you don't mind trading not being as comprehensive as in the Port Royale franchise, and mostly want a sandbox game with huge freedom, by all means, get one of the Space Rangers games (I prefer the second one).

Speaking of M&B and Port Royale together, there is a M&B-based game set in the Caribbean in the making. Called, uh, "Caribbean!" :) Of course, like M&B it is mostly focused on combat, with trading relegated to support roles.

NGDR

If I were you, I'd check Rise of Venice. It seems similiar to Port Royale and Patrician series.