I see that there are hooks for manipulating WP_Query before it gets its posts (parse_query, pre_get_posts), but I can't seem to find any hooks for after the WP_Query object is populated. I have a custom table for my plugin-specific post-associated meta data that I would like to fetch from after a WP_Query object is populated.
As you haven't stated what you are trying to achieve and have just mentioned you need to fetch associated data. You have two options to query your custom table:
The example below demonstrates first method.
For the second method you will need to look at posts_where, posts_join, posts_groupby and posts_orderby filters. As an example you can have a look at the @scribu's sortable custom column's example.