Days ago benchmarks were shared from OpenBenchmarking.org that compared AHCI and IDE modes under Linux when it came to the resulting disk performance. There was a fair amount of interest generated out of that so some AHCI vs. IDE mode comparisons from a Serial ATA 3.0 SSD on an Ubuntu Linux host were benchmarked at Phoronix.
There is really no reason not to use the Advanced Host Controller Interface (AHCI) mode over the legacy IDE mode with the Linux kernel having the necessary support going back to the Linux 2.6.19 kernel. AHCI allows for capabilities such as hot swapping and NCQ (Native Command Queuing).
These benchmarks are from an Ubuntu 12.10 development snapshot with the Linux 3.5 kernel while using an Intel Core i7 3770K "Ivy Bridge" processor with an Intel Z77 motherboard and an OCZ Vertex 3 Serial ATA 3.0 SSD. Between runs, the AHCI/IDE mode was toggled from the BIOS/UEFI. This testing is very straightforward so let us jump right to the results.