do I have to worry about amd graphics card performance on a intel chipsets board
Nope.
I use to like green goblin(nvidia) but heard they not doing good.
Nope. They're fine, could be better, but fine.
What should I be worried about here.
Not much really.
If tessellation is your concern, stick with high-end Fermi cards.
If you are easily bothered by noise/temp but still want high end, 5870 might be better.
If you want the absolute fastest single GPU solution that is non-crossfire/non-SLI, it's the GTX 480
If you want the absolute fastest single card, it's the 5970.
If you are building an expensive rig from scratch, then heat/temps and power should be no concern since it is assumed you are going for a solid case with great airflow and a high-quality PSU. In that case, it is really just your personal threshold for noise that may drive you away from the GTX 470/480. If your room isn't dead-silent, it may be less of a concern (for example, if you've got an industrial fan running in the room anyway, or ambient noise in your house is a bit loud), but it has been known to drive some people to distraction. I don't know how you can find out if it is bearable for you or not outside of trying it out yourself.
EDIT: Forgot to mention, if this is really an expensive, no-holds-barred rig, you may also want to try out a 5970 or 5870 for eyefinity reasons. Having 3 monitors might be a good experience, can't say for myself as I've not had the pleasure of trying it out.