If you only have time to read one article on the current state of al-Qaeda, read the new special report in the Economist. Not only does the author, Anton La Guardia, have great taste (Jihadica and some CTC products I worked on are listed in the sources), but he has done a masterful job of tying together a lot of conflicting trends.
(Note that the links for all of the articles in the report are on the right-hand side of the screen.)