Fortunately, I implemented a cache layer on top of GitHub's API recently, so many examples are working on http://bl.ocks.org. But only those that are lucky enough not to get a connection timeout. Hopefully the API will be back up soon!
Agreed- I've used gists heavily in my blog posts and they look pretty terrible right now. I sent feedback to Github via Twitter. Hopefully they'll fix it quickly.
I'm also a bit sad that they're still using document.write for the embeds. That breaks on any site that uses Ajax-like page loading and is bad practice in general.