Ok, well I will answer your question in reference to graphics - as it seems that is what you are most interested in. I know you have asked about PCI EXPRESS, but I will first explain PCI as that used to be an important part of the equation too.
The PCI (Peripheral Component Interconnect) is a simple way of connecting external components to your machine. Expansion cards (Graphics cards being 1 example) fit into PCI slots on the motherboard, these slots are connected to the CPU (and the rest of the machine via the bus) - the bus allows different data to flow down it from different sources at the same time - so when your graphics card wants to communicate with the CPU (or vica versa) its data gets sent amid lots of other data and often finds itself in a queue. Graphics cards used to use this method of connection prety much exclusively, and it worked well for many years. However, as apps became more graphical the PCI became a point of bottle neck.
AGP (Accelerated Graphics Port) provides a DIRECT connection, from the graphics card to the CPU - there is no use of the bus and as such this channel is execusively for the graphics card. There are additional advantages to this, such as pipelining [where the card can receive and respond to data in one message] and additional bandwidth. These mean that AGP graphics cards are faster than standard PCI and hence replaced it.
PCI Express (a super form of PCI) is centred around the concept of serial links (or lanes) rather than the bus. PCI Express slots can contain from 1 to 32 (as long as 2^n) lanes, the more lanes the better bandwidth available. 16 is the largest size in common use (have a look at your MBoard documentation to see what number lanes it will support.) Here lanes are 2 way, where devices can communicate with CPU and recieve information back at the same time AND lanes can be grouped together for higher bandwidth (so multiple messages can be sent to a device at the same time.) Cards which use PCI Express are most commonly graphics cards but others such as gigabit ethernet are also available too.
Now, PCI Express has replaced AGP prety much and almost all new graphics cards (by NVIDIA and ATI) are PCI-Express. There are some other factors at play (such as the design of the card), but if two cards of the same chipset are available in AGP and PCI Express then the PCI Express one will always be faster.
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