MSI is maybe not the best known brand of Mobos, but they produce great quality. A few years back they were small and had some problems now and then, but today they are a really big manufacturer of motherboards and produce fast, stable and reliable motherboards (for example the MSI K7T pro comes highly recommended for AMD).
Just because Abit and Asus are well known doesn't mean they're the only ones who produce quality motherboards. Chaintech, Epoc and Gigabyte are brands I would not recommend over MSI, though those aren't bad either.
My toplist would be:
Asus / MSI (depending on the type of motherboard)
Hope this eases your mind a bit..