Yeah, the GPU and CPU are really the most important things. It is true that some makes and models perform better than others even if they have the same specs, but MSI is a noteable company and produces solid products.
Look into the MSI-1029 for a good, mid-level gaming computer at an excellent price.
Again, you won't go wrong with the MS-1029. Everything good you hear about it like thin/light/strong build/no flex/brilliant screen etc is true! Got mine with the MT-40 CPU. Playing Half Life 1 source (still an awesome game!), Half Life 2, Guild Wars, Flatout. it's FAST!