Let me explain my reasons a little further in hope of schooling some n00bs.
1) Chassis to engine
This first connection is to connect all of your chassis grounded electronics to the alternator. When the alt supplies the power (POS+) for a device, those electrons must make it back to the source of the power, which is the alt in this case. Most alts do not have a dedicated NEG- post because the entire exterior is the NEG- post. Because it is bolted to the engine, every metal point on the engine is an extension of this same point on the alt case.
2) Chassis to battery NEG-
This is also the end grounding point for all of your electronics that are chassis grounded throughout the car. This is only needed when the front battery is the source of power (POS+) for the given device. So, if your engine is off and the battery is producing the charge, the electrons have to make it back to to the NEG- post of the battery.
3) Engine to battery NEG-
This is the optional one, because if the first two are done, then the engine is in fact already connected to the battery via the chassis. But ask yourself this question; Would a short piece of wire be better than making the power go down one wire to the chassis, around the engine bay through that chassis, up another wire to the battery? This wire will alleviate that long trip through the chassis.
Now this wire is only going to aid in the charging of the front battery. It is not crucial to have this wire like I said, but it does reduce the overall resistance in your grounds. I just prefer to have the shortest path available for any ground in my system.
Remember that the end point of your ground is NOT the chassis, it is the source of the power. Sometimes that source is your alternator, sometimes it is a battery.