A couple of more updates from last night:
UPDATE 9 (1/16, 8:06pm): Nintendo's website listing has now changed from "coming soon" to "pre-order currently unavailable." Don't despair, though: we're still keeping an eye out and will update this post if we see the system for sale anywhere soon—though now that it's the weekend, things may be slower. We'll keep an eye out for GameStop news on Monday. Also, remember, there's always a chance there will be extra systems on the shelves at your local retailer when it comes out next month (February 13).
UPDATE 8 (1/16, 5:07pm): A number of readers have reached out to tell me that GameStop contacted people whose Majora's 3DS orders were rendered incomplete by lag on the website. Those people—who can still get the system—have until Monday to pay in full. If they don't pay, those pre-order slots could reopen for new people, so we'll keep you updated if we see GameStop (or anyone else) taking new orders next week.