The rise of a pair of pants refers to the measurement from the waist of the pants down to the crotch.
Because of the curvature of the material, the rise of a pair of pants cannot be derived from the inseam and outseam, and must be measured directly. The rise of a pair of pants can also be different for the front of the pants to the back of the pants, so it is sometimes expressed as two numbers (the front rise and back rise).
In general, you should get pants that have a rise that is tall enough to be comfortable, but not too baggy. A long rise tends to make the legs seem shorter (since it lowers the crotch), so is not recommended for shorter guys. On the flip side, tall and lanky guys should avoid pants that have really short rises, and go for a taller rise, which will make them look more proportioned.
The rise of pair of pants should not be confused with the terms high-rise or low-rise (as in, low-rise jeans). Rise in this context refers to where the jeans sit on the body. High-rise sit high above the waist, whereas low-rise jeans sit on or below the hips.