it depends on what you do, only one device can communicate on an IDE channel at one time you must remember that, so if you do a lot of transfers between two HDD's you will find that using the HDD's on the separate channels are more beneficial (IDE channel 0, and IDE channel 1), like wise for the optical drives, if you transfer alot of data off of the optical drive to HDD, then having them on separate channels is more beneficial.. (AKA DVD backups ** wink wink ** ), this being that you can make simultaneous transfers over DMA on the two different IDE channels, therefore having the DVD-ROM drive and HDD communicating at the same time.
Ohh, and whether it is on slave or not does not make a difference in performance (Only if the above applies). What DMA mode you are using, and the fact if you are using DMA over PIO is the defining performance hit (DO NOT use PIO)!
NOTE: if you set the primary and slave jumpers on the devices instead of using CS (Cable select), this also improves your POST time, as the BIOS does not have to spend more time detecting the two primary and slave devices.
Kapeesh