Here's an updated list of the sets that have not been found yet in stores or online to my knowledge.
It's not sure these sets will be released at all.
Nickelodeon sets
Mikey Kraang Dunk ( DXY05 )
Raph Slapshot ( DXY06 )
Donnie Baseball ( FFC50 )
Leo Touchdown ( FFC51 )
Shredder's Throne Battle ( FFC57 )
Sewer Battle ( FFC63 )
Shellraiser Showdown ( FFC64 )
Micro Figures (Blind Bags) - Series 6 ( DMX21 )
Half-Shell Heroes sets
Donnie Ooze Roadster ( DXV84 )
Dojo Duel ( DXV85 )
Donnie Mouser Ally ( DXV86 )
Turtle Van ( FFJ48 )