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In fact, this problem is not that simple as it seems. But we'll start with trite things: In pure theory mATX motherboards are smaller and thus cannot carry a large number of integrated controllers, they are equipped with fewer expansion slots and other connectors, they can be installed in small PC cases and consequently they are cheaper. Alas, everything is much worse in practice:
As a result, we have a paradox here: the standard intended for low-end solutions, de facto abandoned its niche... but where did it land? One can say that it landed in the niche of miniature rather than cheap solutions. That's why I recommend mATX only to those who absolutely refuses to bear the sight of this "stupid coffin" (PC case that can fit an ATX motherboard inside), but have no money for a barebone-kit or don't want it because of obviously limited upgradability and still more limited expandability. In fact, a combination of mATX motherboard and a usual (that is really small) mATX case these days is an interim compromise solution between a full-sized desktop and a barebone-kit. mATX borrowed relatively easy upgradability and price from desktop systems and dimensions from barebone-kits. What concerns the compromising nature, mATX is worse at upgradability (expandability) than desktops, it's more expensive (due to PC case), and its dimensions are still larger than those of a barebone-kit. One thing I can say for sure: if PC case dimensions don't matter, you'd better choose an ATX motherboard. And "by contraries": if you don't plan on buying a small PC case, there is no point in buying a mATX motherboard at all. The only exception is that you have already found the model you like, which is much cheaper than its nearest decent counterparts in ATX format.
If we are not going to consider cable colors and printed logos as advantages, we just have to draw a conclusion that comparing motherboard bundles comes to the humdrum comparison of prices. That is if you have to buy additional cables (or something) to your motherboard, then the sum of all additional purchases must be added to the price of the motherboard, to ensure a fair comparison with a competing motherboard with a better package contents. And that's all. Perhaps, the only valuable bonus is Parallel ATA and FDD cables in cambric (see Photo 2). This has nothing to do with easy installation (see "Assemblage convenience" below), they are just less "messy" inside the PC case and thus they contribute to better air flow. Besides, some programs in the bundle may also come in handy. Of course, it's a matter of taste. But other things being equal, I'll choose a motherboard, which comes shipped with something like Norton Internet Security or Power Quest Partition Magic. That is, something useful for me.
It also makes sense to inquire whether the motherboard comes shipped with additional brackets for interface connectors, which are not located on the rear panel of the board. But sometimes a motherboard supports additional USB or COM ports, but the bracket for these ports is not included into the bundle. If these ports are critical to you, will you go fetch the brackets to a computer store? Unless the sales person agrees to expand the bundle in situ – but in this case (remember...) de factor price of additional components should be added to the motherboard price. Thus, the bundle issue is perfectly simple – count the money. Either the money you saved or, vice versa, the money you spent on additional components. Translated user's guides may also be critical to some users, I guess. Though, frankly speaking, I just don't understand how a user will choose componentry and assemble a computer without assistance if he doesn't understand at least technical English.
Though theoretically, OEM motherboards cannot be sold by retail, in practice you keep meeting them at each turn, especially in our parts. I will briefly explain the differences for those who are not familiar with the notions. Retail – a product we are used to seeing in stores: packed in a separate box of a special design (cardboard or foam plastic "inserts" of complex forms, padding, boxes within boxes). This is done with the sole purpose: to reduce mechanical damage of the product to minimum in transit (at least when manufacturer's recommendations are observed). OEM – products, officially intended for computer integrators instead of the retail market. They are not packed into separate boxes, a motherboard with cables is just put into a plastic shipping bag. When in transit, several dozens of bags with motherboards are packed into one large box. The risk of mechanical damage is still low at this stage, because packaging is done by manufacturers, who are interested in safe transit of their products.
However, when a box with OEM boards is unsealed by a large dealer instead of the retailer in order to resell them "by the piece" to smaller stores, how careful the boards are treated depends solely on the fidelity of the large dealer and its clients. Motherboards are often piled in a single box with other ordered components, which sometimes results in physical damages in transit to the destination selling point. Such damage often cannot be detected visually. Moreover, in some nasty cases a motherboard may even retain part of its functions, it will just act "in a strange way". There can be only one conclusion from the above said: if you are offered a motherboard in a plastic bag (or some box of strange appearance and origin) instead of a brand box, this is most likely an OEM board. Thus you risk buying a damaged product. You had better avoid it, even though an OEM version of a motherboard may be a tad cheaper than the same motherboard in retail package.
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