it depends what you want from your mobo.
4x/8x AGP, Max memory, max DIMM size, dual channel? S-ATA, RAID. integrated LAN (usually the case nowadays) and also if your looking at PCI-Express. dont forget to make sure you get the righ socket type.
Asus and Abit are good reputable companies to buy from, i got an Asus and it great.
just look for the features that you need / think u will need in future, look for them mobos that have those and compare between other brands with similar features.