God Eater - July 2015 - multiple special episodes needed, though apparently they at least announced ahead of time that it was going to happen; will need extra slots eventually
Sky Wizards Academy - July 2015 - originally supposed to air in April 2015 but was forced ahead an entire season "due to animation production"
Blood Blockade Battlefront - April 2015 - needed one recap episode, then ran out of available slots to air the final episode (which also apparently went beyond a normal 30-minute slot); will need extra slots eventually
Cinderella Girls - January 2015 - originally planned for straight 2-cours, forced to go split cours
Mushishi S2 - April 2014 and October 2014 - 1st cour needed two specials, ran out of timeslots; 2nd cour started later in its season and the final arc as a movie in Summer 2015 was probably planned ahead of time
Hanamonogatari - August 2014 - originally supposed to air in May, forced delay due to production
Girls und Panzer - October 2012 - two recaps/specials, ran out of timeslots, final two episodes aired March 2013 (three months after)
Eureka Seven AO - April 2012 - three weeks worth of episode delays, ran out of timeslots, final episodes aired November 2012 (though apparently two weeks were for the Olympics so maybe this one was a foregone conclusion)
and a special mention to Wizard Barristers, which while not delayed apparently has massive amounts of animation clearly missing from its final episode (if I recall duckrolls comments properly)