I have an ABIT TH7II-RAID that works very well in LINUX although I don't have LINUX installed on it only Win98. I also have an ABIT KA7-100 that works great in LINUX. Yes, I have LINUX and Win98 installed on the KA7-100. IMO, ABIT motherboards are fast for accessing data from the hard drive than other motherboard manufactures like ASUS.
If I had to get a new motherboard to be used for LINUX. I would get an AMD based board. This is because AMD is much faster than INTEL when it comes to 16-bit code. Most of the open source programs are 16-bit.
NVidia also have LINUX modules for their motherboard chipsets (nforce 415 and nforce2 420), but many people have problems setting up LINUX on those kinds of chipsets. There is enough threads in this forum about those chipsets.
I don't recommend getting any SIS chipsets because you will have the same problems as you did with VIA chipsets.
If you don't mind re-programming your programs to be in 32-bit form and re-compiling the kernel to get some P4 features, you may want to get a P4 system. All 845 chipsets and 850E chipsets have USB version 2 and atleast 4X AGP. For your memory, get a slightly faster memory like DDR433 or faster if you are going at 400 MHz because the speed of the memory will decrease every year.
ABIT's nforce2 motherboards looks very interesting. It may handle Barton processors because of the 3 phrase voltage regulators and 12V ATX (P4) connector.
Below are good sites to check for lateast computer hardware
AnandTech
Hot Hardware
Toms Hardware