There is one question that I always ask before a build regarding motherboards:
How often do I want to replace this motherboard? I recently built a new PC, and I got the Asus 990fx. Part of it is because it was compatible with the AM3 processors as well as the AM3+ processors, so I'm currently running a Phenom II x6 1100 Black edition, and could theoretically put a Bulldozer processor in it a few years from now (once the kinks are worked out). I have the capability for 16 gigs of ram (8 right now), and 3 PCIe ports (of which I'm using 1).
The great thing about the motherboard? I know that, should I need to, I can put more RAM in, add another GPU, even swap out the CPU. I can easily see this board going through 3-4 iterations, depending if my needs change. Plus, it was within my budget and I kinda liked the way it looked.
Now, this might not be a big thing for you if you're not thinking about upgrading in the future with this build. So, keep this in mind: if you'd be willing to buy new parts to replace components for this build 2-3 years from now, you should get motherboard that exceeds your current needs, and has lots of headroom. Buying one $200 motherboard might not be as cost-effective as buying two $75 ones, but it is a lot of hassle, and then on top of that you need to play the "are all my old components going to work with the new motherboard" game (not fun to realize that buying your new Mobo means needing to replace all of your RAM chips and finding out your sound card won't work anymore). Not to mention taking everything OUT of the case, then putting it all back IN, because suddenly the cable run is two inches to short all of a sudden (grrrrr)
However, if you're just building for someone else who isn't going to have their needs change, I would say "just go for one that you can put more RAM in later." If you're building an "economy" system, you probably know it will never be able to keep up with system requirements, so you can skimp on stuff in the short term.
So, when looking at your mobo choices, think about how often you'd seriously want to swap it out. If you're planning on swapping/upgrading/adding components in the future, go for the mobo that has support for the newest (and even future) tech that's within your budget, and supports the other tech you plan on putting in it.
If you're just going for the cheapest buy you can, well, go with that.
If you're down to two very similar boards, you might just end up being in a "pick one" or "compare the check boxes" situation.
Except for obvious situations, there isn't really a right answer for "which mobo is the right one for me". If you think about what you're going to use it for, and how often you're going to be fiddling with the other components in the system, that will lead you towards your answer.