There are (at least) two other things that cause open edges that you haven't mentioned. I do a lot of fixing of open edges for people, and these are just as common as the faces being flipped.
I have demonstrated this on the following model:
[ATTACH=full]86618[/ATTACH]
The line on the left is caused by two vertices not lining up in the middle of the line. As the vertices don't line up, the faces on either side of the line are not connected.
The lines on the right are caused what I like to call a "hidden face", a face that sits fully inside the model (technically it can be on the outside, but it will be a lot more obvious). Pepakura designer can only work with one continuous surface, meaning that any line that is connected to more than two faces will be causing open edges.
Same model viewed in Blender:
[ATTACH=full]86619[/ATTACH]
The solution to the problem on the left is to make the two vertices in the middle match up, and remove doubles. The solution to the problem to the right is to delete the edge underlined in green. This will effectively remove the inside face (seen as a darker surface while in wireframe mode) and no open edges will occur.
[ATTACH=full]86620[/ATTACH]
