Most often, the SATA controller (JMicron, Silicon Image). Some network cards also cause problems (Marvell Yukon).
For the SATA controller I recommend using AHCI mode in the BIOS for maximum compatibility, but it depends.
For the network card, it's best to disable it if you have problems and buy a better one. There may be ways to work around issues tho, it will just take some time.