A motherboard's main job is to act as a conduit
between the various hardware elements that make up a PC. It needs
to be able to link the desired CPU(s), system memory, graphics card,
hard drive(s), and add-in cards and enable them to work in harmony.
Thinking of the way in which a motherboard is laid out, the central
brain of any motherboard, the chipset, usually split into north
and southbridges, is connected to the rest of the system via a number
of links. It's some of these links/buses that have been improved
over the last 18 months or so since the introduction of the PCI-Express
architecture.
History
Up until the emergence of PCI-Express, motherboards' chipsets
were connected to one another via, usually, proprietory links that
allowed data to flow between parts of the system. The northbridge
was connected to the CPU via some form of front-side bus and, on
the other side, to system memory at varying speeds. Finishing off
a trio of high-speed buses was a link to a discrete graphics card,
up to AGP 8x, which offered a point-to-point 32-bit, 66MHz connection
with bandwidth totalling 2.13GB/s (32x66x8).
The southbridge was hooked up to the motherboard's storage subsystem
and, in terms of expansion, most boards offered up to 6 32-bit 33MHz
slots that were run via the PCI bus. Doing the basic maths tells
us that the PCI bus offered up to 132MB/s bandwidth. The inherent
problem, though, was one of sharing, as all devices attached to
it had to share this 132MB/s. The quoted bandwidth was fine when
devices, even when run concurrently, required low bandwidth to function,
but, over time, add-in cards or discrete board-mounted ASICs' bandwidth
requirement has grown considerably.
Newer bandwidth-eating technologies like Gigabit LAN, FireWire
support, discrete SATA support, and RAID cards can each, theoretically,
swamp PCI's bandwidth quota individually, let alone collectively.
To get around this, chipset designers had to architect southbridges
with an increasing number of the aforementioned technologies already
amalgamated on-chip. This, however, was just skirting the obvious
shortcomings with the established PCI bus protocol. What was needed
was another type of bus that would be both smarter and have the
ability to scale as devices and board features became faster over
time. For a time the PCI bus' longevity was thought to lie with
PCI-X (not be confused with PCI-Express), which was simply a doubling
of the bus speed to 266MB/s, achieved by increasing the bus width
to 64 bits instead of 32. That, though, was simply a stopgap measure
to keep the status quo intact.
Championed by Intel and debuting for the consumer-level market
in 2004 came the long-awaited successor to the ailing PCI bus interconnect.
Enter PCI-Express.
PCI-Express
Unlike the shared-bus nature of PCI, PCI-Express (a.k.a.
PCIe) is a serial, point-to-point connection that has the added
benefit of being bi-directional in nature. The point-to-point, dedicated
connection between any pair of devices is referred to as a link,
and the connection itself as a lane. The intrinsic beauty of PCIe
is that each lane can transmit, bi-directionally, 250MB/s. That
already makes it faster than a 32-bit PCI bus and takes away the
need for devices to share a single bus. Further, PCIe lanes can
be grouped together for transfers at higher speeds and a x16 lane,
made up of 16 lanes, has the ability to signal data at 4GB/s, again
bi-directionally, which beats out the 2.13GB/s afforded by AGP.
Therefore not only is PCIe more elegant than PCI and AGP, it can
be made to be faster than both, and as discrete graphics card become
faster and faster, the ability to move masses of data around from
CPU and main memory becomes increasingly important. Taking this
into account and appreciating that PCIe is based on a bus architecture,
a x16 PCIe lane makes for a better conduit than AGP, not only in
terms of sheer bandwidth but also with respect to the bus' ability
to run more than one card in a single system (SLI and CrossFire,
anyone?) The bi-directional nature of PCIe also makes it a decent
candidate to take the place of a third system bus, the interconnect
between chipset bridges. That's not to say that the PCI/AGP mainboard
architecture simply isn't working well right now; it is, but the
escalation of hardware speeds is such that another inteconnect system
is needed, and that's PCIe in a nutshell.
General application
Intel first brought PCI-Express to consumer-level motherboards
in 2004 with its 900-series of chipsets. Intel also realised that
whilst PCIe was better than the combined talents of the incumbent
PCI and AGP buses, motherboard simply couldn't eschew PCI immediately;
too many users and ASIC companies had money invested in PCI-based
hardware, so the first foray into modernising the archaic PCI architecture
was an exercise in compromise. Since then, NVIDIA, VIA, SiS, amongst
others, have designed chipsets that take advantage of the present
and future benefits provided by PCIe, and it's now become a common
sight on all modern chipsets for Intel and AMD's processors. Motherboards
have a fixed number of total PCIe lanes available, ranging from
around 20, and most 'boards will contain at least a single x16 lane
that's usually reserved for graphics card usage. The remainder of
lanes are designated for either inter-chipset connectivity or for
the relevant buses pertaining to hardware expansion.
In conjunction with general chipset re-design, the suitability
of PCIe, in x16 form, as a graphics card bus has seen industry heavyweights
NVIDIA and ATI consequently shift their GPUs' interfaces from AGP
to PCIe. Indeed, look at any etailer's discrete graphics card catalogue
and PCIe-based cards will now outnumber their AGP counterparts,
and the vast majority of new GPUs coming out the fabs are now packaged
in PCIe form. The downside for the enthusiast is the barriers of
entry for a full PCIe-based motherboard. Coming from a decent AGP-based
system and wanting to 'upgrade' to PCIe, you will need to invest
in not only a new motherboard but also in a new graphics card, unless
you're prepared to opt for a one of the few chipsets that amalgamates
PCIe for discrete hardware and AGP for graphics.

Motherboard implementation
If we take a look at an Intel D955XBK as an example of a
PCI-Express-based motherboard, we see that the two long-ish ports
to the left of the northbridge support dual x16 slots, intended to
be used with PCIe-based graphics cards. The lane-building and true
bus nature of PCIe has opened up the possibility of GPU manufacturers
to design multi-GPU setups that just weren't possible with AGP. NVIDIA
took the first step with its SLI technology and ATI has followed with
its version, named CrossFire, and both require the presence of two
x16 (lengthwise) slots In this case, the D955XBK is a CrossFire-certified
motherboard and the second x16 slot, to the left, when used concurrently
with the right-hand one and with two compliant ATI CrossFire-based
cards, offers up some lovely multi-GPU fun.
Most motherboards with dual x16 physical slots remap the second
slot down to PCIe x8 (that's still 2GB/s, bi-directionally), although
the newest iteration of Intel i955x chipset-based boards now offer
true dual x16 support. Continuing the theme of PCIe as a means of
running multi-GPUs, ATI's CrossFire and NVIDIA's SLI both require
certified motherboards on which to run two or more cards concurrently.
It's a company-specific and not PCI-orientated issue. Motherboards
with a single x16 slot, which tend to be the majority, will only
support a single card, obviously
PCIe speeds range from x1, x2, x4, x8, and, of course, x16, with
each number representing the number of bi-directional lanes present
in the link. In terms of hardware expansion, a x1 lane, shown by
the small slot to the right of the three regular PCI's, will accommodate
discrete cards that are slowly coming to market. Often, motherboard
designers will take up x1 lanes by integrating a PCIe-based ASIC
on the board itself, usually along the lines of SATA RAID (Silicon
Image Sil3132, for example), Gigabit Ethernet, or FireWire support.
The future
The introduction of PCI-Express has remedied the bandwidth
and architectural limitations imposed by the old PCI bus and AGP
interface. Thanks to its multi-lane nature and as a suitable bus
for graphics cards, it's also opened up the way for multi-GPU goodness
not seen since the days of 3dfX and its PCI bus-sharing SLI. If
you're contemplating a new system, wish to build it yourself and
want it to be as future-proof as possible, PCI-Express really is
the only way to go.