Mostly for gaming but i will be programing alot of things on this comp as well. I use Photoshop, powerpoint, exel, openoffice, Network Visualizer, Router Esim, Packet tracer, and DivX alot. And once and a while i configur cisco routers.
Exhaustive list. I had my share of Cisco config as well a few years back, ethereal is your best friend.
Since you'll be gaming, no sense in getting the one with the built-in video, since you'll be buying a more powerful card anyway. Be aware that the realtec 883 codec on both boards sucks big time. On a basic, cheap, 2 speaker stereo setup it may sound ok, but if you try to use a quality 5.1 or above speaker system you'll notice lots of background noise and hissing. The HD codecs are passable, but the ones they call "High Quality", basically a marketing stunt to trick you into thinking it's HD, are really bad.
Other than that, I dont see any major reason to go with one over the other. I assume the main reason you're going AMD is to make a cheaper system (with a 100$ single-core athlon) ? Otherwise there's better value on the market right now.
Personally, I'm a fan of the Gigabyte board. Since the feature sets/prices are very similar, I personally would go with the Gigabyte due to the manufacturer's willingness to help in the case of problems. I have had to deal with both companies in the past, and the Gigabyte was definitely easier to deal with, and MSI definitely didn't want to help me with my warranty claim.
The MSI does have VGA/DVI outputs built in though, if that matters to you.