Which StackExchange site if preferred when asking questions specific to Apple hardware, but concerning running Ubuntu?
Specific example, would be "how to get hardware component X of MacBook Pro running in Ubuntu XX.YY?".
If the question is about Apple hardware, I would ask the question on Ask Different.
If the question is about the Ubuntu driver to use for specific hardware, then I would ask the question on Ask Ubuntu, or Super User if the correct answer could be given from who has experience with both Mac OS software and Ubuntu software.
It would really depend on your question—if it's more about Ubuntu, and you're just incidentally running it on Apple hardware, I would go with Ask Ubuntu. On the other hand, if it's more a hardware problem, Ask Different might be the better place, but I would also seriously consider Super User. Without more information, I'm afraid it's really hard to say exactly which site would consider it on topic.