I'm looking at 2 motherboards that will do most of what I need. One is a ASRock Micro ATX 880GM-LE @ $59 (Newegg) and a MSI 880G-E45 ATX @ $99 (Newegg). I believe the Micro ATX will fit my case. The reason for picking these 2 boards is Floppy support that I need as discussed in another thread.
At nearly half the price, what's the downside to getting a Micro ATX board vs a ATX other than it being smaller?
None. Micro-atx has fewer expansion slots, but some folks don't ever use them. Check the chipset video driver if you use onboard video. Also check the "cpu support" section to see which cpus you can upgrade to later. I always upgrade the cpu and board at the same time, but some folks want to save money. Future proofing is tough to predict, since changes are happening every 18-24 months.