Micro ATX boards have fewer PCI slots (usually 3 vs 5). They use the same
chipsets, and many have all the features available on a standard ATX board.
If you want on board graphics, it's easier to find on a microATX board.
I've built two computers based on the Biostar M7NCG board, which is micro.
It's the NForce 2 chipset with on board graphics (with an available AGP slot
for video card upgrade), sound, LAN, USB2, and headers for firewire. I built
them for my kids and did not have to add any additional PCI components. Both
have been running about a year with absolutely no problems.
Fitz