$re = '/^(\[\^)([^\]\s\p{C}]+)(\])\ (\P{C}*(?:\n(?!\n[\[\n])\P{C}*)*)/m';
$str = 'Pseudo-example:
Sentence of the first [^a]paragraph. Sentence[^b] of the first[^b] paragraph[^1]. Sentence of the first[^1] paragraph. Sentence[^1] of the first paragraph. Sentence of the first paragraph. Sentence of the first paragraph. Sentence of the first paragraph.
[^a] Sentence of a long margin note\'s body that refers to the word "paragraph".
[^1] Sentence of the first paragraph of the footnote. Sentence of the first paragraph of the footnote. Sentence of the first paragraph of the footnote. Sentence of the first paragraph of the footnote.
Sentence of the second paragraph of the footnote. Sentence of the second paragraph of the footnote. Sentence of the second paragraph of the footnote. Sentence of the second paragraph of the footnote.
Sentence of the third and the last paragraph of the footnote and two empty lines after it!
Sentence[^1] of the second paragraph. Sentence of the second paragraph. Sentence of the second paragraph. Sentence of the second paragraph. Sentence of the second paragraph. Sentence of the second paragraph. Sentence of the second paragraph.
[^b] Footnote at the end of the file. Footnote at the end of the file. Footnote at the end of the file.';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php