Bonded ground/neutral
If you have the neutral and ground bonded at a subpanel, then you'll get neutral return current through the ground wire back to the main panel (since there are now multiple paths). Even worse, as @Tester101 points out, if the neutral ever has a fault, everything will continue to work but you'll have all the current on the ground, which also means that you can now be electrocuted by touching the panel chassis, for example.
The ground and neutral must be bonded only at one place (in the main panel) to avoid this.
Subpanel main breaker
A main breaker on a sub-panel is not necessary because this is in the same building (if you are in a different building then NEC 225.31, 225.32, 225.33 apply). That said, having a main breaker in the sub-panel is also acceptable.
For whatever reason (economy of scale, I guess) "main" panels are often sold cheaper. I recently purchased a small 12-breaker panel (which included a main breaker and a couple 15A breakers) for almost half the price of a similarly-sized sub-panel (which didn't include any breakers). It makes absolutely no difference to wiring, you just have to be sure to take out the ground/neutral bonding screw/bar (if pre-installed).
Subpanel ground
The sub panel must absolutely have ground back to the main panel, and it must be appropriately sized for the current rating of the panel (as in, it's the same as or larger size than the hot/neutral wiring). This is regardless of being in the same structure or not.
The three wire allowance is an exception to 250.32(B)(1), which allows existing installations that were compliant with previous code versions to exist. If you want to bring the installation up to current standards, you can install a properly sized grounding conductor between the panels and separate the neutral and grounding bars in the second panel.
The reason you need to bond the neutral bar in the case of a three wire feeder, is to provide an effective ground-fault current path. Remember, electricity is trying to return to the source, not to the ground (earth). In the event of a ground-fault, you want the fault current to be able to have a low resistance path back to the source. This low resistance path should allow the fault current to be great enough, so that a circuit breaker (or other protective device) can activate and open the circuit.
If you read the text of the code, you'll find that it says "the grounded conductor run with the supply to the building or structure shall be permitted to serve as the ground-fault return path". By bonding the grounded (neutral) and grounding bars in the panel, you're using the grounded (neutral) conductor as a ground-fault return path.
Hope this makes sense, and answers all your questions.
Best Answer
We don't build the system for normal circumstances. If we did, we wouldn't need circuit breakers, would we? :)
Ever hear of a "Lost Neutral" situation? This is where neutral becomes loose or broken, and is no longer pegged in the middle at 0V between the two opposite 120V phases (or at 0V in between the three 230V phases in Europe). Neutral is subject to a "tug-of-war" amongst the various phases - the more load on a phase, the harder it pulls. This causes the weaker phase's voltage to go higher than spec, which often burns out equipment.
Suffice it to say, neutral is no longer at 0V, and could be as high as 120V or 230V if only a single appliance is turned on (or still functioning).
Now, what would happen if the ground was attached to that lost neutral, i.e. the chassis of all equipment? Well that would be at a high voltage along with the neutral, and people would be getting nailed off switch plate cover screws.
That's... why you maintain ground separately at all points beyond the main disconnect.