Generally, Stack Overflow is fine, but as random pointed out in his comment, it depends what is being asked:
GitHub is certainly a tool commonly used by programmers, per the FAQ. I like to think one of the best ways to decide what to ask is to first observe what is being asked and answered well by the community.
(This should also explain why things that are popular for the wrong reasons, that are opinion pieces rather than science, are deeply problematic at SE.)
Since you specified
suppose it's a question about github-style docs, or repository organization
That implies it could be opinion-y, or a bit too specific to GitHub's own peculiarities. Overall though GitHub is so overwhelmingly a programmer site that some opinion and/or specificity to GitHub is likely to be OK.
And it turns out the GitHub guys concur with Jeff! From the announcement where they shut down their Google Groups group:
After three glorious years, we're shutting down this Google Group next Monday, May 9th, 2011.
You can always contact Official GitHub Support by emailing sup...@github.com or visiting https://github.com/contact
As for unofficial help, we recommend Stack Overflow: https://stackoverflow.com/questions/tagged/github
If you're referring to the Web interface, then certainly WebApps.SE. WebApps.SE deals explicitly with web applications as accessed by users of the application. If you're referring to Git, or SSH, as end user applications on your own system that merely access GitHub servers then certainly Super User. If you're referring to an API, or integration with GitHub by way of something like OAuth -- then probably Stack Overflow. And, lastly, if you want to get away from them and run your own clone or start a centralized Git endpoint then perhaps Server Fault which deals with server administration.
Stack Exchange has a high learning curve. To figure this kind of stuff out it usually takes a lot of use. If you ask in the wrong place and the moderators don't like the question and catch it within an arbitrary time frame, your questions may be migrated. That's no problem. Don't forget you can always read the specific site's FAQ by clicking
FAQ at the bottom of the screen. The FAQ will tell you what is on-topic and not on-topic. As a last resort, you can always send a quick e-mail to firstname.lastname@example.org and ask them for an authoritative decree.
As of now there are only 92 sites on the Stack Exchange network to choose from. It's probably worth it to just take a day out and read all of their