Constrain connecting lines to be only horizontal or vertical (only 90º increments) in OmniGraffle?
With the Line Tool selected you can begin drawing your line and then press the SHIFT key. At this point, with both the mouse button and SHIFT key down, the line will restrict to 45-degree increments.

When dealing with a connection line, where the line's start and end point are linked to an object, it become more difficult. The line's orientation is based on the location of the object's line anchors. You will need to make sure that the anchors your line is attached to are aligned appropriately. This can normally be done through the standard object alignment tools.