Hmm... Okay. First, the larger problems I noticed...
As previously mentioned, when you go to 'controls' in the main menu, then back, it doesn't clear the controls.
In the town there seems to be some grass tiles that you can't walk on, and the collision detection on the tree to the northwest of where you start is... well, it's like a huge square that's too big for the tree.
The top line of pixels and the left column seem to randomly clear/not clear, and the whole screen seems to move one pixel down and right when a battle occurs-- then back when it ends. The music doesn't loop, which gets rather annoying... It's jarring when it suddenly ends, and then after playing for awhile you forget about it, only to be startled when it suddenly comes back in in another scene.
Collision detection in general is a bit annoying-- for example, say you're walking up along a vertical wall, (and it's on your right) and you hold right and up at the same time, you'll stop. Single-tile doors are difficult to get into due to the collision detection, and once I went in a door only to be transported to the other end of the room I was supposed to be in, confusing me greatly for a moment. There was also a man who I could not talk to in this room, apparently randomly placed there.
Health goes into the negative when someone dies. They still act as if they are alive. I mean... I'm fairly sure that'd be an easy one to fix. When I got to the boss of the castle, Jeremy stayed behind the door but was still in battle-- When I tried to attack with him the game crashed. I could still choose options, but nothing did anything anymore.
Now the smaller issues, nitpicks mainly.
It is sometimes difficult to tell whether chests are open or not... As they only move one or two pixels when open. Sometimes when going into battle you will be sideways when it occurs; the sword sprite looks rather odd this way and you sort of slide sideways to attack. These are mostly tiny issues, but you may want to think about more frames for your walking animations. They don't look too much like walking as it is...
Hope I didn't sound too harsh, but I did find quite a few issues... I hope you fix some of these in final version, as I heard quite a bit of praise for the eventual plot of the game awhile back. However, if these problems remain I don't know if I'd have the patience to play through it as a finished game.