As of kernel 2.6.25, sata_sil24 supports Silicon Image chipsets 3124, 3131, 3132, and 3531, including OEM rebadges from Adaptec.
Summary: Full TCQ/NCQ support, with full SATA control including hotplug and PM.
Use the Sil3124 if available as it is a nice, open design.
If a card using this driver does not seem to present individual drives to the system's BIOS for bootup purposes, re-flashing the card to the "base" (non-"raid") bios may resolve the issue. Despite documentation that says to choose "JBOD" in the raid firmware for this purpose, that option does not seem to exist in recent revisions. Card firmware is available from Silicon Image
Hardware flashing hints
PLEASE NOTE: NB: flashing a rom image is an advanced procedure.
PCI-X (64 bit PCI) cards such as SYBA 40009 may need to be placed temporarily in a 5V PCI (32 bit) slot in order to flash successfully, as some flash memory requires 5V to program.
During POST, the flashed card may not display any information on screen, or may very briefly display information about connected drives. This does not seem to affect operation.
Commonly available environments that may work to perform the firmware change: Knoppix live disks can boot freedos, which can then run the Silicon Image flash utility. Flashrom, a utility from the coreboot project may be used to flash the rom if freedos is not available. Live disks including flashrom likely include Knoppix and Partition Magic.