Tsubasa Reservoir Chronicle and it spin-off., xxxHolic.. If you haven't read thess., try.. From the half part., the plot becomes much darker..
For non-bl try these along with the ones Kaheru mentioned -
http://www.mangago.me/read-manga/onani_master_kurosawa/
http://www.mangago.me/read-manga/kimi_no_knife/
http://www.mangago.me/read-manga/sugiru_juunana_no_haru/
http://www.mangago.me/read-manga/monster/
http://www.mangago.me/read-manga/skyhigh/
http://www.mangago.me/read-manga/confidential_confessions/
http://www.mangago.me/read-manga/delivery/
http://www.mangago.me/read-manga/life
http://www.mangago.me/read-manga/gunslinger_girl/
http://www.mangago.me/read-manga/pet_shop_of_horrors/
Some have HIGHLY disturbing contents. So Please check the tags before reading.
Any plot heavy manga? It doesn't have to be yaoi or shounen ai (unless you have any to rec)
Thanks!