Well, I've built computers, but never totally from new components. That is, there were always some parts I already had that I wanted to use. When you're doing that, you have to keep a close eye on what the mobo will work with, like memory, CPU, IDE interfaces, number of PCI slots, etc..
I try to keep an eye on upgrade potential too. Like nowadays, you can still buy Socket A CPUs and motherboards, but their days are numbered. So unless I had a higher-end Socket A CPU with nothing to do, I would steer clear of a Slot A motherboard. Replacing a motherboard is enough of a pain so you want to do it with an eye to the future. I go for technology that is old enough so that it's not real expensive, but new enough that it's not obsolete a year from now.
I've had good luck with ECS and MSI, but I think most brands are pretty reliable if treated well.