I think that AHCI is a tossup depending upon your hardware. For example, on my computer with a Gigabyte GA-EP45-UD3R Rev 1.1 mobo with the F9 BIOS...when you enable AHCI you are presented with an 8 second delay on each and every reboot as the system initializes the controller. In addition, with tools such as HDTune and HDTach, when AHCI is enabled my read and write speeds drop by a few MB/s.
And the "potential benefits" from NCQ don't seem to actually make hardly any difference whatsoever based on a bunch of timing tests, reboots, and benchmarks.
Therefore, I know that I lose exactly 8 seconds at each boot and I don't believe that I gain those 8 seconds back within an hour or two of using the computer from NCQ.....so for this reason I leave my computer in IDE mode and feel it provides the best performance with my configuration.