Yes, you will need a Apple spec'ed HD to replace your current HD if that is your Q.
If you are thinking of adding a 2nd drive, Apple has indeed gone with a up-coming PCIe connection for the SSD port over their propriety SSD connection (still not ratified so it could end up being unique to Apple). It's intended to support a SSD not a HD. Besides the 21.5" model just doesn't have the space inside to hold a second traditional 2.5" HD. Even a SATA SSD will need to be one of the barebones types. The good news is on the 21.5" systems Apple has put the SSD connector in (if you buy a HD only unit) so you can add it in later (the late '11 models don't have it).
I'm not sure even if the new 'Thin' iMac 27" has any space to spare for a 2.5" HD either you might be able to mount one of the super thin drives just coming out or maybe a smaller iPod type drive but these thin or ultra small drives are not very fast or large Vs a SSD. At least right now.