As I mentioned I highly recommend a Pentium M based system which I believe is an 855GME chipset or something like that. Definately works with Windows 98 and it's about the fastest thing you'll be able to get to run Windows 98 without jumping through a lot of hoops.
Your not going to find anything brand new that still supports Windows 98 unless it is New Old Stock. Personally what I would do is go to ebay. Look under motherboards and CPU/Motherboard combo sections and just search for miniITX. Skip over all the listings that are too blatantly new then google for drivers for the chipset to see if there are any Windows 98 ones out there. Or better yet post some of the ones you are looking at on this thread and someone might comment if they have had good luck with them or not.
Basically I would start out with figuring out what you can find first, then see if it will work with 98, rather then asking people what they are using only to find out you won't even be able to find it.