When I was designing my board, I was using the program inkscape, which doesn't allow you to disable anti-aliasing. This doesn't make the board upload look pretty, and it takes editing to try and make the board look better, but its not perfect. It would be really awesome if I could adjust the fill tolerance in the Board Designer. e.g. its currently set to 0%, at 100% it would fill the whole board, at 50% it would recognize colors with 50% similarity.

Would be interesting to see if that could be worked into the Designer, and could potentially help with a lot of first time boards.

Side note, have you looked into Paint.net?

I have, but unfortunately, I can't find a decent alternative for Mac Users...

What about GIMP? I know it's available for Mac, but I haven't used it much so I'm not too sure of its features/limitations.

Try Acorn.  I can't remember what I paid for it, but I'm pretty sure it wasn't a bank-breaker.   Also, if you need a little help with it, I might be able to help..

GIMP can do just about everything.

There's no flexibility with fill tolerance in either JS or Flash so this one's not going to happen I'm afraid.