Coloring shapes with the Fill inspector
Use the Fill inspector to choose a color or gradient to fill the inside of the selected shapes.
The Fill checkbox determines whether the shape should have a fill at all. When it is selected, controls for choosing the type of fill become available. 
Use the pop-up menu on the left side of the inspector to choose from the five kinds of fill: Solid, Linear Blend, Radial Blend, Double Linear Blend, and Double Radial Blend. 
The blend rotation control becomes active when you choose a linear blend; enter a number of degrees in the field or drag the circular control to set the angle of the gradient. The blend position control becomes active when you choose a radial gradient; drag its crosshair to move the gradient's center. 
Click the color well to choose the color of the fill. 
If you have chosen a two-color blend, you can click the swap button to exchange the two colors. 
If you choose a blend, two or three color wells become available. Click them to choose the colors to blend together. 
Drag the bias slider on the far right to shift a blend toward one side or the other. You can also edit the fill color of a canvas itself. Just click the canvas in the sidebar (so that it becomes highlighted in your selection color), then use the Fill inspector normally.
OmniGraffle Pro offers an extra section in the Color panel for creating pattern fills.