About the only sure fire find out whether or motherboard is 100% working is that it's the only item that you have not replaced yet.
Good Old Fashion Get Your Hands Dirty Trouble Shooting.
I normally change over the RAM, CPU, CARD and try getting the machine to boot up with the bare minium first. It's the idea of "We Changed Every Thing Else, It Has To Be The Motherboard"
Then again, I got the recourses to able to swap and change hardware at my work (Computer Store). Eg. Spare parts and a working test bed.
Because Changing a motherboard is one of those tasks I loath doing, I try checking every thing else first.
As for software for checking your motherboard, contact your motherboard's manufacturer. They MAY have some thing that you can download. Some how I dought it as the last thing the manufacturer's really needs in all there end users who thing they "know-everything-about-computers" bugging them.
Trust me, I had enough bad expereinces with end users and fault finding software just because they don't what they are doing.
About the only thing that i can think of that get remotely close to what might be after is a P.O.S.T. CARD. It's a PCI card with an Display that will test your PC for faults when booting up.
The only problem is.... the cheap ones (approx AU$500) will only tell you the obvious (eg. No Ram, No Video Card, IDE Channel Conflict etc.). These ones are a complete waste of time as your POST beeps and 5 minutes of reading the motherboard manual will tell you the same thing.
The ones that really work (eg. The ones that will tell you give you the details on what part of the motherboard is wrong) are start at about AU$2500. At that price, you can buy yourself another motherboard with a kick ass system on top of it.