I'm running a CentOS server and I'd like to replace the existing motherboard. Everything else in the system will stay the same. Basically, it's an entry level Dell server in a standard ATX tower. I'd like to rack mount the server, but Dell doesn't offer a rack mount kit for my server model. Also the Dell has a proprietary motherboard and heatsink that doesn't fit in my standard ATX rack mountable case. The only way to get the machine to fit, is to just swap out the mobo.

So, how does Linux handle a motherboard change? I know windows can freak out if you change the chipset. How does linux do with this sort of thing?

The only thing that could happen is that the Sound/Network/Graphics wont work. But even so you can reconfigure them.
Make sure you plug the hdds in right though.

so Linux doesn't have a hard time detecting the new chipset drivers? that's a relief, windows always get's all pissy.

Not at all. You can actually switch harddrives arround in different machines and they usually boot fine, not recommended tho.