Recently I posted about the problems I was having with Aquaria not scaling properly when using the 1280x960 resolution on my 1280x1024 monitor (many modern LCDs use a 5:4 aspect ratio - it's actually non-widescreen).
Well - I found a very simple (and "clean" - you only edit a configuration file) workaround - I wonder why Alec hasn't mentioned this:
Go to your Aquaria folder and open init.cfg with the notepad or any other plain text editor.
You'll find a line similar to this one:
1280 960 32 1 1 0 255 0 0 1 1 0
As you can see the first three numbers represent the horizontal and vertical resolution and the color depth.
I (obviously) changed the line to:
1280 1024 32 1 1 0 255 0 0 1 1 0
Et voila! It works perfectly although the image is stretched a bit.