General preferences
On Startup Select Remember open documents if, every time you open OmniGraffle, you'd like to see the same documents you had open the last time you quit.
Select Remember open stencils to see the same stencils you had open the last time you quit.
Select Create new document if nothing else is open to start with a new document when you aren't making OmniGraffle remember open documents, or if there were no open documents the last time you quit.
Text Editing Decide how you would like the Return and Tab keys to behave while you are editing an object's text. Whichever way you choose, you can hold Option while pressing the key to do the reverse instead.
Line Creation When you are creating a line, clicking an object will always connect the line to the object and end the line. If you click in an empty area of the canvas, though, you might want to end the line there or you might want just to add a point there and continue creating the line. Use this preference setting to indicate which you prefer.
Line Label Creation When you double-click a line, you might prefer to add a new point to the line, or you might prefer to add a label. Choose one; Option-double-click will do the other.
Selection Small objects get smaller versions of the handles that appear when you select them; if you really like the small ones, you can use them all the time.
When you click in the middle of a shape object that isn't filled with an image or color, you might want to select the object or you might want to select whatever is behind it. Use the Click through objects with no fill checkbox to indicate which you prefer.
Help Tags When you move or resize an object, a little help tag appears to let you know the object's new location and size exactly. That is, unless you find it annoying and turn it off here.
Backup OmniGraffle can periodically save a backup of your files as you work on them; if something unfortunate happens you can then recover some of your work.