I would personally(and do, actually) use Gigabyte. Their boards are faster(check benchmarks) and more stable and have the best warranty of any boards on the market. That said MSI also makes some NICE boards. Just be sure you use good chipsets, and a solid board. That said, 229 really isn't nessecary(especially when that board is 160 at newegg...229 is overcharging). My personal recommendationw ould be something like:
or this http://www.newegg.com/Product/Produc...82E16813130527
But have a look here, some people like other brands like DFI party, eVGA, Abit and others. Just check around do a little research, you will find a nice board.
ASUS was the best years ago, kind of like Soyo they had their day in the sun, and since then aren't what they once were. As for windows dependence, I hadn't heard that, but I suppose anything is possible with the upcoming Vista campaign.