IDE is the name of a disk controller. Other types of disk controllers include RAID, SCSI, and AHCI.
Which mode is better depends on what you want to do with it. For instance, if you want to run a RAID array, you will have to use a RAID controller. You can generally select the controller you want to use in your system's BIOS.
For general, all purpose use, IDE is fine. AHCI offers some improvements to IDE, but in typical use, you probably wouldn't notice a difference.
I presume you are talking about the SATA port mode setting in your BIOS Setup screens. The answer you need depends on the version of Windows you are using, and how you are using the hard drive.
SATA drives are best used as AHCI devices and, when possible, that's the way to set their port modes. HOWEVER, there are limits. The main one is that Windows up to XP in all forms does NOT know how to handle AHCI devices unless you install a driver for it. Win Vista and Win 7 have no problem with AHCI - they have the required drivers built in.
So, if you have Vista or Win 7, go into your BIOS Setup screens, find where the SATA port modes are set, and change them to AHCI. Save and Exit and it should just boot up fine and look like nothing has changed. There are subtle improvements in disk operations behind the scenes.
In a few cases when you make this change Windows chokes and can't boot and run. No big problem. Just reboot back into BIOS Setup and change the modes back to IDE (or PATA) Emulation, Save and Exit.
Now, IF you are running Win XP and this is your boot drive, do NOT make this change. The reason your BIOS has a port mode known as IDE (or PATA) Emulation is so it can fool Win XP into thinking the real SATA drive is actually an plain old IDE drive it understands, and XP is happy to work with that. If your XP was installed that way, you cannot change it without doing a complete re-install, so don't try unless you really have a good reason.
A few people have XP as their OS and want to set up a second or third drive which is NOT used for booting as an AHCI device. That can be done in BIOS for those particular drives, but NOT for the boot drive. Then you MUST install in Win XP the required AHCI driver (check your mobo's CD disk or the maker's website for the driver) and reboot so that XP can use the AHCI device. BUT this does not let XP use that driver to BOOT from, so you must leave the C: drive as an IDE Emulated device.