Shipping costs? why are we comparing something homebrew to something OEM? Of course the hardware is going to be A LOT cheaper for them. If you accounted for the cost of the hardware if you were an OEM + overhead + profit, the iMAC would seem like a terrible deal. However comparing it to a homebrew solution requires you to account for individual shipping, reseller markup, manufactuer markup, shipping, and possibly taxes.
Software wise, OEMs have an ability to get things at a very reduced rate. Perhaps because they "want" their products inside dells, etc... At home you must pay full price, where as an OEM may even get away with paying very little to nothing by allowing a lite/OEM version of their product to be installed.
Though, much of the software that you are suggesting has free alternatives, they might not be compariblity to the iLife software in terms of userability, this is why you buy software, because you want something that works for you. With the MAC you have your hardware, much of the software(at least you are paying for it), and almost all of the customization(hardware wise) left up to MAC.
Trying to compare these two platforms in terms of cost is pointless. A lot of people feel that Mac's are a $2000 wastes of money. However people who like them and use them find that the cost gets them everything they want. For them that is fine. However there are many people who are not satisfied by it, and would rather create their own, no matter how much the cost. They may have to suffer at having a small(there are very small computer cases for pentium M desktops if you want them) case next to their monitor(that they can keep through major upgrades). I for one would choose the PC I built, but not everyone would. Not everyone should, they arnt right for everyone, and for some you would have to comprimise on what you actually wanted.