Arrange menu
Bring to Front / Bring Forward Objects on the same layer have an order to them: newly created objects appear in front of objects that already existed. Select Bring to Front to move the selected objects in front of all other objects on the layer.
Hold Option to change this command to Bring Forward, which moves the selected objects forward one step in the ordering.
Send to Back / Send Backward This works like Bring to Front, except it moves the selected objects behind all other objects on the layer.
Hold Option to change this command to Send Backward, which moves the selected objects backward one step in the ordering.
Lock Lock the selected objects. A locked object can't be moved or edited. When you try to select a locked object, it shows X marks instead of selection handles. Really, the only thing you can do with a locked object is unlock it; the exception is that you can change an object's label and hierarchical position from the outline view. Locking is useful for making sure you don't accidentally change something you had set up just right.
Unlock Unlock the selected objects so that they can be moved or edited.
Group Use this command with at least two objects selected to turn them into a group. A group behaves like a single object.
Ungroup Use this command with a group selected to separate it back into its component objects.
Make Table Use this command with one object selected to turn the object into a 1x1 table, to which you can then add rows and columns.
Guides OmniGraffle offers smart guides and manual guides. Smart guides are little blue lines that appear as you move, resize, or rotate objects; they help you keep objects aligned and spaced evenly. Manual guides are canvas-spanning magenta lines that you place yourself; you can make as many as you like, use them to align objects, and show or hide them from the View menu.
Enable/Disable Smart Alignment Guides — These are the smart guides that appear to help you line up objects' edges or centers. They also help you match objects' rotation when you Command-drag an object's selection handles.
Enable/Disable Smart Distance Guides — These are the smart guides that help you space out objects evenly.
Lock/Unlock Guides — As long as the guides are locked, you won't be able to move them.
New Horizontal/Vertical Guide — This puts a guide across the canvas; if the guides are not locked you can use the Selection tool to drag it into position wherever you like. As you drag an object near a guide, its edges or center snap into place along the guide.
Clear Manual Guides — Remove all of the manual guides from the canvas. If you just want to temporarily hide them, you can do so from the View menu.
Align These commands replicate the functionality of buttons in the Canvas: Alignment inspector, lining up objects' edges and centers, or spacing objects out evenly.
Grid Snap to Grid and Align Objects to Grid work just like they do on the Canvas: Grid inspector; Size Objects to Grid resizes objects to make their edges follow the nearest grid lines.
Size With more than one object selected, you can make the objects the same height, width, or both. Make Natural Size makes an object's height and width equal. For objects with an image placed in the Style: Image inspector, Size to Fit Image makes the object big enough to show the whole image at its original size.