Where is the best online design store?  

A couple
Apartment Therapy keeps a really good list: http://apartmenttherapy.com/ny/stores/
My personal favorites are 1stdibs.com and my own: eboniste.com

PORCHMODERN.COMwww.porchmodern.com is rather nice.

Cimmermann
This is a really cool store - check it out for classic to modern day design.
http://www.cimmermann.co.uk

design store on line
Easy, best on line store,Panik in Milton Keynes,excellent delivery also!!.

Design Within Reach (DWR.com...
Design Within Reach (DWR.com is a big one, not sure if they are one of the best but they really put themselves out there.

Zeitgeist Modern Furniture
I like Zeitgeist Modern Furniture Classics www.z-mfc.com

I will contribute a few
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Great thread, learned some new ones to add to my book marks (Btw, don't underestimate DWR, great store.).
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So I will contribute...
Moss http://www.mossonline.com
House of European Design http://www.design-eu.com/index.htm
Minima Home http://www.minima.us/index.html
Bo Concept http://www.boconcept.com
ligne roset http://www.ligne-roset.com
Surrounding Lighting Interiors and Accessories http://www.surrounding.com/
Obviously the MoMA store: http://momastore.org
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Some other resources that are not necessarily "stores"-
Moco Loco http://www.mocoloco.com/
RE.Luct http://www.reluct.com
Stylepark http://www.stylepark.com
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Moss
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Did I mention Moss?
Oh, yes I did.
Moss http://www.mossonline.com
I'll sell it twice.
Dont' let its simplicity fool you. The site drills down pretty deep, with quite a bit of inventory.
cheers
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Oh, and the navigation...
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Oh, and the navigation can a bit un-intuitive Minima. Roll over the red word "product" in the lower left (if you have a large monitor, and the window is opne large, it can get lost down there).
http://www.minima.us/
cheers again... now I'll f*ck-off and get some sleep.
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here are some from me http://www.moderncollections.com/http://www.whiteonwhite.com/xoops/xoops-2.0.9.2/html/modules/news/http://www.naos.net/http://www.cierreimbottiti.com/http://www.desalto.it/english/english.htmhttp://www.moroso.it/http://www.vitra.com/

Yes, DWR has helped furnish my apt.
I've shopped with them for a long time.

DWR sales
I've got several items from DWR. With few exceptions, most of the items I've gotten were on sale. While some of their discount were hardly (read: only 10 percent off), I was able to purchase a coffee table and end table from DWR for more than 50 percent off their regular retail, and a noguchi lamp for about 20 percent off their regular retail.
Personally, I love ebay and, for new items, www.highbrowfurniture.com (free shipping!). If you are buying Herman Miller items, it does pay to purchase in June or December frow Highbrow. HM items are discounted 10 percent during those months, which, coupled with free shipping, is not, comparatively speaking, a bad deal.

If DWR has helped you furnish...
If DWR has helped you furnish your apt, then I assume that your income is pretty high! Most people I know save a lot of money to buy one or 2 items from them but not for the whole apt, good for you. I live in the bay area, which is where DWR started, so I had the fortune of attending several of their sample sales at their main warehouse. Their name, Design Within Reach, merely means they will bring high design to you, it doesn't been it's "Within" your budget unfortunate, however, it's still a great store.

I wish . . . .
I had a high income. I'm not rich; just a smart shopper who regularly checks sales/clearances at my favorite online stores. In fact, the coffee and side tables I got at DWR were $160 and $90, respectively. And a bistro table was about $250.
While I agree that most items at DWR are hardly "within reach," there are definitely deals to be had at DWR, particularly on smaller items. DWR whacks you bad with their shipping costs. It's too bad you can't pick up items at their studios.