I have just started looking at how to make extensions, but to implement some vital bbcode extensions for my site it seems I need hooks in parser.php (yes I know it is being rewritten, but thought you might like to know some suggested locations):
Line 34, After "$smiley_img" lines so more smileys can be added
Line 320 and 329, In do_bbcode(), after $pattern and $replace arrays, so new bbcode tags can be implemented
Line 365, In do_smilies(), after "$text = preg_replace(..." inside loop so more smileys can be implemented
Line 379, In parse_message(), after "$text = censor_words($text);" so I can pre-parse some tags
Line 413, In parse_message(), after "$text = str_replace($pattern, $replace, $text);" so I can parse a tag
Line 425, In parse_message(), after "if (isset($inside[$i])) {" before "$text .= '</p><div class=..." as I need to undo the math tag inside code tags.
Line 429, In parse_message(), before "// Add paragraph tag...", which is the correct place for another tag
And whatever standard place you would include new functions