I had a cheap ATX case a few years back that had a headphone/mic jacks in front.  The connectors for this setup wasn't a pin base motherboard type plug, but rather a regular mic/line-in/heaphone jack type plug that ran through the inside of the case and would go out the PCI slot opening and plug into the back of the computer.  I tried my headphones and mic into them and both suffered from terrible noise interference.  A constant humming/buzz.  I attributed it to the case since the front panel jacks has it's own circuit board and I assumed it was bad or of really bad quality.
My new case has front audio jacks (with motherboard plugs), but I do not use them because I would have to use my onboard sound.  I can't stand the lower quality of onboard sound system.  Some people don't mind it, but I'm a self acclaimed audiophile.  My headphones have a 3m cord IIRC and easily reaches to the front of my desk.