It's usually the Motherboard. Sometimes online you can find CPU/Motherboard combos to lighten the price. RAM can be pretty expensive also. Hard drives are around the same price as ram and so are Graphics cards.
A nice motherboard cures many ills and is the foundation of your rig, now, and in the future. AND, if you play by the rules your OEM operating system is keyed to it, so you may as well invest in a nice one.
Expensive mother boards are only if you want to do alot of upgrading and get the last bit from your overclock. If you will put together a system and leave it then just get the cheapest (but a reasonable make) that has the features you need, the money is better spent on a better CPU or GPU.