When meta- is typically prefixed to something being used as a technical term, it roughly means "higher ordered".
This means that if there is a sequence which itself contains a sequence, one can talk about the internal sequence as a "higher ordered" sequence or a "meta-sequence".
As ggambett mentions, Meta-StackOverflow is for discussion about StackOverflow. StackOverflow is only about discussing programming problems, while the higher-order discussion is about discussing the discussion of programming problems.
Likewise if one were to try to talk about the commentary on StackOverflow in a similar manner, it could easily be construed as meta-meta-StackOverflow discussion.