Question: I am going to buy my first proper road bike, and I have been comparing entry-level carbon frames with top-level aluminum frames in the same series (Giant Defy). What are the benefits of carbon vs. aluminum frames? Is it better to get an aluminum bike with higher-end components or a similarly priced carbon bike with lower-end components?

Answer: 
One thing that I have found is you can usually get a lighter weight bike if you go with top-level aluminum over a low-level carbon. The low-level carbon frames tend to have a lot of fiberglass mixed in to keep the cost down and the components are much cheaper too which will weigh a lot more. I think it's kind of funny that everyone looks down on my aluminum bike and yet it weighs less than their carbon bikes that cost twice as much! I have owned carbon, steel and aluminum bikes
Quality-wise bikes are a lot like chains. The total quality of a bike (where with quality I mean stuff like durability, smoothness, ease of use, ease of maintenance, etc.) is very dependent on the weakest link.

An expensive frame with cheap components makes for a worse bike than a mid-range frame with mid-range components. So given the choice I'd go for the (relatively) cheaper frame with the (relatively) more expensive components, all dependend on what I actually wanted to spend on the bike.

There are "ride quality" differences between carbon and aluminium and steel. Carbon is usually less stiff, so the ride is a bit more comfortable. Steel has the same properties as carbon and is more durable, aliminium is usually a lot stiffer and hence the ride is harsher. For that reason you get aluminium frames with carbon fork and stays. The main disadvantage of steel is of course weight, but you have to look at this critically. The 0.5-1 kg weight reduction you get by going from a really good and durable steel to a carbon frame disappears in the 15-20 kg of fat you are lugging around anyway, and unless you plan to go ride a lot of serious races you will never notcie the small gain of the lighter frame.

Where I'm going with this: In the standard bikes you buy the frame is often of higher quality (and price) compared to the other components. You can get a better bike for less money if you pay attention to this when buying your bike. Spending some time talking this over with you friendly LBS owner will help here.