I've made an enhancement so the hexes can be turned 90 degrees. You can now to orient the map in a "true columns" way (so the hexes form columns--the way it was before) or as "true rows." (If you have a better idea for how to name these two map orientations please let me know.)
There's an option on the initial Hexographer program window (the one that runs in the browser) to switch between these two map orientations. When maps are saved, this property is recorded so when you reload the map it will be set appropriately. You can also switch this property when you are viewing a map by going to the "Options" menu and choosing one of the "Hex Orientation" options. (But I wouldn't recommend it for maps that already have lines drawn. The change will cause those lines to not match up with your terrain.)
I've also added a "pan" button in the bottom left corner that allows a user to easily drag the map to move it and replaced a few of the text buttons with icons.
Also, previously I added a feature so hexes can be customized. The icon in a hex can be resized relative to the hex's size or the icon can even be turned off and the background color can be changed.
Here's the link since the old one is a couple of pages back: Hexographer