Here is my first attempt at listing unfinished threads in the game. Feel free to add your own!

Monastery:
Beach - looks like there is a way to explore the ocean

Arnika:
Boat dock and boat
Lighthouse
Boarded up house
Higardi/Tremain - seems useless

Trynton:
Ocean - shouldn't there be something there besides fish?
Martens Pagoda

Wilderness Clearing: (or is it SE Wilderness?)
Fountain with fish - should do something
Temple tomb - should have a catacomb or puzzle

Rapax areas:
Queen - at least be able to rescue her
Kings Assassins - should be a subplot, w/queen?

I'm sure I'm missing a few...

I think something was meant to be in the swamp, too. There's an area with a number of fallen trees against it. It really looks like you should be able to walk up one of those trees and get inside, but you can't. I spent a lot of time trying that before I finally decided this was another dead end.

<center>Nightowl2</center>

The mook
you should be able to enter the ship

there should be a final fight on asenscion peak between your allies and enemies. Im pretty sure its supposed to happen in the landslide.

Endings with Umpani and T'rang.
Marten's Pagoda is nothing I believe
Swamp was supposed to have many things, but budget cuts :( .
Rattus ending never finished (IMO, he would join you)

Here is a nice link from RPGdot with a small discussion that might add to conversation.
http://www.rpgdot.com/phpBB2/viewtopic.php?t=34218

The computer in the Arnika Jail seems like it should do something.

What about the diamond? Wasn't that supposed to be part of the 'Miles Quest' portion of the game? Any of you ever pick up a 'dead frog'?

The diamond is part of a quest. It was stolen and you can return it.

There are a number of useless items in the game. I think the dead frog is one of 'em. Like the rubber shoe (yes, one shoe)

Is there ANYTHING that can be done with the Mook ship in Arnika? I've been wasting a lot of time wondering around it, looking for stuff to do, and I keep drawing a blank. I put the damaged black box in the computer system, but it can't read it anyway. Should I be wasting any more time with this, or would I be better off just moving along?

Nope. Sorry to say, the Mook ship is a dead end. There is no use for the damaged black box, either.

<center>Nightowl2</center>

you will return there when you find an 'undamaged' black box. But for now, no theres nothing to do there.