Actually I change my opinion after doing a bit more research. I would suggest you use the HDA where you can. I think I will change my case at home now.
The AC'97 connector simply extends the audio card's or motherboard's microphone and speaker to the jack on the front of the Antec or other manufacturer's case.
The HDA has additional functionality to enable "jack sensing", meaning on audio cards or motherboards with more sophisticated sound systems a popup will show prompting you to select what it was that you just plugged in. For example, it will ask if you want the connection you just made to be a "line out" or a headphone. Or whether it is a "line in" or a microphone.
HDA stands for high def audio, and you can look into it further if you like.http://www.intel.com/design/chipsets/hdaudio.htm
Here is a webpage you may find useful and informative as well.