I traded my 03X for an 06 and it has a sticker that says I can hook up my Ipod to it. I just dont know where the hell to connect it at. Does anyone know how to do this or is there some special items I have to buy to do this??

you need a cable that connects the headphone jack to the AUX input spot on the actual stereo itself. Also it is probably described somewhere in the owners manual or the "quick reference" guide that came in your little binder with the owners manual, warranty guide, lemon law book and so forth.

Will this work for all 06's? I got the S (not the premium sound RF system) and wonder if I'll be able to hook an iPod up (if I ever get one) to it.

That's awesome! I wonder if they'll make all Nissans with the iPod hook up? The more I read about the X the more I want it.

I have an 04 xterra and I just use an FM transmitter.

I assume they are trying to get you to buy this part:
Linky
which would plug into the back of the RockFos head unit.

Or are they implying that you can plug an ipod into the existing setup with out buying anything? If you don't have to buy anything, they just snuck a very nice upgrade into the middle of the production year! (unlikely!)

Edit/Disclaimer - that link shows part assuming you do not have factory satellite setup. There's a different part# if you do have pre-installed satellite module.

You'll probably see just about every new vehicle come with a auxilary input jack.