Footnotes in custom fields

I think that what you need to do is find where your custom meta data is displayed and do this:

echo jqFootnotes(get_post_meta($post_id, $key, $single));

That will run the jqFootnotes filter on your post meta, and I think that will do what you need (assuming that $post_id, $key, and $single are set appropriately)..

Side note: just because there is a the_content() function and a the_content filter doesn’t mean that you can use any function name as a filter. Most functions do not have a matching filter.

For reference: http://codex.wordpress.org/Function_Reference/apply_filters

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