These two chipsets are important to consider when you are looking to buy a motherboard, especially when you are looking to build a free and open source based machine (for example FreeBSD or linux).
The north bridge is what connects the cpu to the RAM, and potentially the AGP graphics card.
The south bridge is what connects the cpu to the PCI bus and your peripherals, including your network and your disk I/O controller (PATA, SATA, SCSI, or SAS).
If you plan on doing as much networking as I do, then both bridges are very important, and the south bridge to the network can be a challenge to get working properly. First off, there are two pieces here, the southbridge chipset and the actual network interface chipset, both of which need to be considered. Here's an incomplete list of chipset manufacturers:
SouthBridge Chipset Manufacturers
Networking Chipset Manufacturers
As I said earlier, this is an incomplete list of southbridge and network chipset manufacturers - there's a lot out there to choose from!
For disk IO, I mostly use software based RAID setups, which leverage the CPU's processing power, so you won't find me grappling with the south bridge chipset trying to get hardware RAID working. Most of the time, southbridge chipsets are what are known as "fakeraid", meaning they end up using software configurations anyway, and leverage the CPU to do the heavy lifting. You can also use a hardware based RAID solution, which if its a "real hardware raid", will work great too.
Ubuntu has been doing a great job raising awareness about the "openness" of video cards, but what about network chipsets? First and foremost, here's a big thank you to Donald Becker who wrote and released a lot of open source network drivers! Second, kudos to Intel for recognizing the marketplace and opening their drivers. Here's a list of manufacturers who have contributed code to open source networking device driver projects:
http://www.hailfinger.org/carldani/linux/patches/forcedeth/ - author of the Nvidia forcedeth driver, to which Nvidia contributed to years afterwards for gigabit support
http://www.dailywireless.org/2006/12/28/open-source-wifi-drivers/ - good list of open source wifi drivers, as well as those manufacturers who won't allow freebsd to distribute firmware for :-( I was surprised to see Intel in the offenders list, but its interesting to see these companies going the open route: Amtel, Zylink, and Zydas.