What is the advantage/disadvantage of doing this over using only 2 channels to power front and rear?
The advantage is that you will have fade and balance for all four speakers. If you used 2 channels for four speakers you would lose either your fade or your balance depending on how you set it up.
Also, if you have four speakers and a subwoofer, what is the advantage/disadvantage of using 2 channels to power the 4 speakers (F,R), and then bridging the last two to power the sub vs. buying another mono amp just for the subwoofer?
The same comment I made earlier about fade/balance for the speakers. As far as the sub is concerned, a mono amp is always a better choice for subs (IMO) as they are designed to amplify only the lower frequency spectrum and are much more efficient than a typical class AB amp design. Most mono sub amps tend to be Class D amps.
If you want 4 speakers and a sub each speaker needs individual amplification. Trying to parallel your lefts to a 2 ohm load and then trying to run the fronts on a 4 channel to your left and etc. is just not a good idea. It is definitely do-able in theory (but hell, so is socialism) but I wouldn't recommend.
If an amplifier is rated at say 100w X 4, does that mean for each channel it can push 100watts for a total of 400w?
An amplifier rated @ 100W X 4 into 4 ohms will give you 4 seperate channels that produce "100" watts at 4 ohms. As you may notice from the quotes I consider most power ratings to be marketing tools and would recommend you ignore them for the most part. I always love the guy who asks about the 1800W 2 - channel BOSS amp for like 40 bucks and they say it has more power than an RF or kenwood with a "little more" of a conservative rating. Side note: I'm waiting to see whether or not this new CEA-2006 rating standard means anything. We'll see.