As far as I'm away PCI Express is used for Small Form Factor cases, like some of the Dell Optiplex. These are the smaller tower units, often used in offices and the like, and they probably won't fit in a standard tower case.
PCI Express is used as a high speed (bandwidth) replacement for AGP as far as graphics cards are concerned. They are for use in desktop or tower PCs as well as small form factor PCs.
Motherboards are still being made in PCI Express and AGP flavours. If a motherboard is designed to take a PCI Express graphics card, it will specify that it has a PCI-E 16x slot.